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24 lines
1.6 KiB
Markdown
24 lines
1.6 KiB
Markdown
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# Semantic Description of `obialign` Package
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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**:
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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.
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- **`encodeValues(score, length int, out bool)`**:
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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.
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- **`decodeValues(value uint64)`**:
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Reverses encoding: extracts score, reconstructs original length via `((value + 1) ^ mask)`, and checks the out-flag.
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- **Utility Bitwise Helpers**:
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- `_incpath(value)`: decrements stored length (since it's negated, subtraction increases actual path).
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- `_incscore(value)`: increments score by `1 << wsize`.
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- `_setout(value)`: clears the out-flag, marking value as *not* terminal.
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- **Predefined Constants**:
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- `_empty`: neutral state (score=0, length=0).
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- `_out`/`_notavail`: sentinel values for invalid or unavailable paths (high length, score=0).
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This compact representation enables fast comparisons and updates during dynamic programming or alignment graph traversal—critical for scalability in large-scale metabarcoding analyses.
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