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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)
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1.3 KiB
Semantic Description of obialign Package
The obialign package provides low-level utilities for efficient nucleotide sequence encoding and decoding, specifically designed for bioinformatics alignment tasks.
- Core functionality: Encodes IUPAC nucleotide symbols (including ambiguous codes like
R,Y,N) into compact 4-bit binary representations. - Binary encoding scheme: Each bit in a byte corresponds to one canonical nucleotide: A (bit 0), C (bit 1), G (bit 2), T (bit 3).
- Ambiguity support: Codes like
R(A/G) set both corresponding bits (0b0101). Fully ambiguousNsets all four bits (0b1111). - Gap/missing handling: Symbols
.and-, as well as non-nucleotide characters, map to0b0000. - Memory efficiency: The encoding avoids allocations via optional buffer reuse.
- Lookup tables:
_FourBitsBaseCode: Maps ASCII nucleotide characters (lowercased vianuc & 31) to their binary code._FourBitsBaseDecode: Inverse mapping for human-readable output (not exported, used internally).
- Integration: Works with
obiseq.BioSequence, a generic biological sequence container from the OBITools4 ecosystem.
The Encode4bits function enables fast, space-efficient sequence processing—ideal for high-throughput sequencing data where alignment speed and memory usage are critical.