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)
1.6 KiB
Semantic Description of obialign Package
The obialign package provides low-level utilities for efficiently encoding, decoding, and manipulating alignment-related metrics—specifically score, path length, and an out-flag—within compact 64-bit integers. This design supports high-performance operations in sequence alignment pipelines (e.g., OBITools4).
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Core Encoding Strategy:
Auint64encodes three fields: a score (upper bits), an inverted path length, and a single-bit flag indicating whether the value represents an "out" (i.e., terminal/invalid) state. -
encodeValues(score, length int, out bool):
Packsscore,-length-1(to preserve ordering via unsigned comparison), and theoutflag into one integer. The most significant bit (bit 32) marks out-values. -
decodeValues(value uint64):
Reverses encoding: extracts score, reconstructs original length via((value + 1) ^ mask), and checks the out-flag. -
Utility Bitwise Helpers:
_incpath(value): decrements stored length (since it's negated, subtraction increases actual path)._incscore(value): increments score by1 << wsize._setout(value): clears the out-flag, marking value as not terminal.
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Predefined Constants:
_empty: neutral state (score=0, length=0)._out/_notavail: sentinel values for invalid or unavailable paths (high length, score=0).
This compact representation enables fast comparisons and updates during dynamic programming or alignment graph traversal—critical for scalability in large-scale metabarcoding analyses.