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https://github.com/metabarcoding/obitools4.git
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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)
27 lines
1.6 KiB
Markdown
27 lines
1.6 KiB
Markdown
# Semantic Description of `obialign` Package
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This Go package provides core utilities for **DNA sequence alignment scoring**, leveraging probabilistic models and log-space computations to ensure numerical stability.
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## Key Functionalities
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- **Four-bit nucleotide encoding**: Uses `_FourBitsBaseCode` (implied but not shown) to encode DNA bases as 4-bit values, enabling bitwise operations for fast comparison.
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- **Bitwise match ratio (`_MatchRatio`)**: Computes a normalized overlap score between two encoded bases by counting shared bits, adjusting for presence/absence in each operand.
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- **Log-space arithmetic helpers**:
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- `_Logaddexp`: Stable computation of `log(exp(a) + exp(b))`.
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- `_Log1mexp`, `_Logdiffexp`: Accurate log-domain operations for `log(1 − exp(a))` and `log(exp(a) − exp(b))`, critical for probability transformations.
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- **Match/mismatch scoring (`_MatchScoreRatio`)**:
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- Derives log-probability-based scores for observed matches/mismatches using Phred-quality inputs (`QF`, `QR`).
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- Incorporates base composition priors (e.g., uniform 4-mer assumption via `log(3)`, `log(4)`).
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- **Precomputed scoring matrices**:
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- `_NucPartMatch`: Precomputes match ratios for all base-pair combinations.
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- `_NucScorePartMatch{Match,Mismatch}`: Stores integer-scaled alignment scores (×10) for all Phred-quality pairs, enabling fast lookup during dynamic programming.
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- **Thread-safe initialization**:
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- `_InitDNAScoreMatrix` ensures one-time setup of all matrices using a mutex guard, preventing race conditions.
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All computations are designed for high performance and numerical robustness in large-scale sequence alignment tasks.
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