Operations¶

Module-level functions. All operations are plain functions after the FLOF dissolution — no protocols remain.

Operations turn raw data into Tracks. They're the bridge between I/O (genomes, reads, sequences) and the Track-based processing layers (transform, compare).

Operations¶

Operation	Functions	Purpose
Map	`regex_map()`, `bowtie_map()`	Find sequence patterns in genomes
Annotate	`annotate_features()`, `annotate_chromatin()`	Enrich regions with genomic context
Quantify	`count_barcodes()`, `summarize_features()`	Count barcodes or summarize features
Discover	`heuristic_discover()`, `tnseq_discover()`	Auto-detect read structure
Score	`score_mismatches()`, `score_off_targets()`	Score variant effects

Pages¶

Map¶

regex_map — IUPAC pattern matching
Bowtie Mapping — Bowtie alignment

Annotate¶

Locus Annotation — Gene feature annotation
Chromatin — Chromatin state annotation

Discover¶

Read Structure — ReadStructure dataclass
Heuristic — Auto-detect barcode structure
Tn-seq — Auto-detect transposon flanks

Quantify¶

Barcode Counting — Exact barcode counting

Score¶

Mismatch — Mismatch variant scoring
Weights — Load mismatch weight matrices

Filter¶

Overlap — Filter by geometric overlap (recipe-level function)