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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)
20 lines
1.4 KiB
Plaintext
20 lines
1.4 KiB
Plaintext
```markdown
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# DNA Scoring and Matching Utilities in `obialign`
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This module provides low-level utilities for computing nucleotide alignment scores using probabilistic and bit-encoded representations.
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- **Bit Encoding**: Nucleotides are encoded in 4-bit groups (e.g., `A=0b0001`, `C=0b0010`, etc.), enabling efficient bitwise comparison.
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- **`_MatchRatio(a, b)`**: Computes a normalized match ratio between two encoded bytes based on shared bits:
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`ratio = common_bits / (bits_in_a × bits_in_b)`.
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- **`_FourBitsCount`**: Precomputed lookup table for Hamming weight (popcount) of 4-bit values.
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- **Log-space Arithmetic**: Helper functions (`_Logaddexp`, `_Logdiffexp`, `_Log1mexp`) ensure numerical stability in probabilistic computations.
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- **Phred-scaled Quality Integration**:
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`_MatchScoreRatio(QF, QR)` derives log-odds match/mismatch scores from Phred quality values (`QF`, `QR`), modeling sequencing error probabilities.
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- **Precomputed Matrices**:
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- `_NucPartMatch[i][j]`: Match ratios for all nucleotide pairs (from 4-bit codes).
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- `_NucScorePartMatchMatch/Mismatch[i][j]`: Integer-scaled match/mismatch scores (×10) for quality pairs `(i, j)` in `[0..99]`.
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- **Thread-Safe Initialization**: `_InitDNAScoreMatrix()` ensures one-time, synchronized initialization of all scoring tables via a mutex.
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Designed for high-performance alignment kernels where speed and numerical robustness are critical.
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```
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