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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)
23 lines
1.5 KiB
Markdown
23 lines
1.5 KiB
Markdown
# `obialign` Package: Sequence Alignment Utilities
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The `obialign` package provides core functions for pairwise biological sequence alignment in Go, designed to work with `obiseq.BioSequence` objects.
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- **Core Alignment Construction**: `_BuildAlignment()` and `BuildAlignment()` reconstruct aligned sequences from a precomputed alignment path (e.g., output by dynamic programming). It supports gap characters and reuses buffers for efficiency.
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- **Quality-Aware Consensus Building**: `BuildQualityConsensus()` generates a consensus sequence from an alignment and per-base quality scores:
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- At mismatches, it retains the higher-quality base.
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- When qualities are equal and bases differ, an IUPAC ambiguity code is used (via `_FourBitsBaseCode`/`_Decode`).
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- Quality values are combined and adjusted for mismatches using a Phred-like error probability model.
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- Optionally records mismatch statistics in sequence attributes.
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- **Performance & Memory Efficiency**: Uses preallocated buffers (via `PEAlignArena`) or fallback allocation, with slice recycling to minimize GC pressure.
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- **Metadata Handling**: Preserves sequence IDs and definitions in output; supports optional mismatch reporting for downstream analysis.
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- **Alignment Path Format**: The path is a sequence of signed integers encoding:
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- Negative steps → deletions in seqB (insertion in A),
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- Positive steps → insertions in B,
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- Consecutive pairs encode match/mismatch runs.
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This package is part of the OBITools4 ecosystem, targeting high-throughput amplicon or metagenomic data processing.
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