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Eric Coissac 8c7017a99d ⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

2026-04-13 13:34:53 +02:00

Sequence Predicate Framework in `obiseq`

This Go package provides a flexible and composable predicate system for filtering biological sequences (BioSequence) based on diverse criteria.

Core Concepts

SequencePredicate: A function type func(*BioSequence) bool, enabling conditional logic on sequences.
Predicate Composition: Supports logical operations (And, Or, Xor, Not) and chaining.
Paired-end Support: Predicates can be adapted to consider read pairs via PredicateOnPaired and PairedPredicat, with modes:
- ForwardOnly: Only the forward read is evaluated.
- ReverseOnly, And, Or, AndNot, Xor: Combine forward and reverse evaluations.

Predicate	Description
`HasAttribute(name)`	Checks if a sequence has an annotation with the given name.
`IsAttributeMatch(name, pattern)`	Tests if a named annotation matches the provided regex (case-sensitive).
`IsMoreAbundantOrEqualTo(count)` / `IsLessAbundantOrEqualTo(count)`	Filters by sequence abundance (count field).
`IsLongerOrEqualTo(length)` / `IsShorterOrEqualTo(length)`	Filters by sequence length.
`OccurInAtleast(sample, n)`	Checks if the sequence appears in at least n samples (via description stats).
`IsSequenceMatch(pattern)`	Matches the raw sequence against a regex (case-insensitive).
`IsDefinitionMatch(pattern)`	Matches the definition/description line against a regex.
`IsIdMatch(pattern)` / `IsIdIn(ids...)`	Filters by sequence ID using regex or explicit set.
`ExpressionPredicat(expression)`	Evaluates a custom boolean expression (via OBILang) using annotations and sequence metadata.

Null-safe: nil predicates are handled gracefully in compositions.
Extensible: Custom predicates can be defined and combined seamlessly.
Logging & Safety: Invalid regex patterns or expression syntax trigger fatal errors; runtime evaluation issues emit warnings.

This framework enables powerful, declarative filtering pipelines for high-throughput sequencing data analysis.