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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)
21 lines
1.3 KiB
Markdown
21 lines
1.3 KiB
Markdown
# Semantic Description of `obiseq` Comparison Functions
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The `obiseq` package provides utility functions for comparing biological sequence records (`*BioSequence`) based on different fields. These comparators are designed to support sorting, deduplication, or grouping operations in bioinformatics workflows.
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- **`CompareSequence(a, b *BioSequence) int`**
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Compares the raw nucleotide or amino acid sequences (`a.sequence`) lexicographically using `bytes.Compare`. Returns:
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- `<0` if `a < b`,
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- `0` if equal,
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- `>0` if `a > b`.
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- **`CompareQuality(a, b *BioSequence) int`**
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Compares the base quality scores (`a.qualities`) lexicographically (as byte strings), following same semantics as above. Useful for sorting reads by quality profiles.
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- **Commented-out `CompareAttributeBuilder(key string)`**
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A planned higher-order function to generate custom comparators based on sequence attributes (e.g., `RG`, `NM`). It would:
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- Extract attribute values using `.GetAttribute(key)`.
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- Handle missing attributes (treat absent as "less than" present).
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- Eventually support typed comparisons for ordered types.
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These functions assume `BioSequence` implements a consistent internal structure with `.sequence []byte` and `.qualities []byte`. They enable flexible, field-based ordering in collections of sequencing records.
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