mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 12:00:39 +00:00
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)
24 lines
1.6 KiB
Markdown
24 lines
1.6 KiB
Markdown
# 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).
|
|
|
|
- **Core Encoding Strategy**:
|
|
A `uint64` encodes 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)`**:
|
|
Packs `score`, `-length-1` (to preserve ordering via unsigned comparison), and the `out` flag 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 by `1 << wsize`.
|
|
- `_setout(value)`: clears the out-flag, marking value as *not* terminal.
|
|
|
|
- **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.
|