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)
2.0 KiB
Apat Package: Pattern Matching for Biological Sequences
The obiapat Go package provides high-performance pattern matching over biological sequences using the Apat algorithm, a C-based implementation wrapped in Go. It supports fuzzy matching (with mismatches and indels), reverse-complement patterns, memory-safe resource management via finalizers, and efficient filtering of non-overlapping matches.
Core Types
ApatPattern: Represents a compiled pattern (up to 64 bp), supporting IUPAC ambiguity codes (W,[AT]), negated bases (!A), and fixed positions (#).ApatSequence: Wraps a biological sequence (fromobiseq.BioSequence) for fast matching, with optional circular topology support and memory recycling.
Key Functions & Methods
MakeApatPattern(pattern string, errormax int, allowsIndel bool): Compiles a pattern with max error tolerance and optional indels.ReverseComplement(): Returns the reverse-complemented pattern (useful for DNA strand symmetry).FindAllIndex(...): Returns all matches as[start, end, errors], supporting partial sequence searches.IsMatching(...): Boolean check for presence of at least one match in a region.BestMatch(...): Finds the best (lowest-error) match, with local realignment for indel-containing patterns.FilterBestMatch(...): Returns non-overlapping matches, prioritizing lower-error occurrences.AllMatches(...): Filters and refines all valid matches (including indel-aware alignment).Free(),Len(): Explicit memory cleanup and length queries.
Implementation Notes
Internally, the package uses cgo to interface with C structures (Pattern, Seq) allocated via custom memory management. Finalizers ensure safe deallocation, while unsafe pointer arithmetic avoids data copying during search (e.g., unsafe.SliceData). Logging is integrated via Logrus.
This package enables scalable, low-level pattern mining in NGS data preprocessing pipelines (e.g., primer detection, adapter trimming).