API Reference¶

rusty-dot exposes its functionality through the following classes and functions.

Classes¶

Class	Module	Description
`SequenceIndex`	`rusty_dot`	Rust-backed FM-index for sequence comparison
`DotPlotter`	`rusty_dot.dotplot`	All-vs-all dotplot visualisation
`CrossIndex`	`rusty_dot.paf_io`	Multi-group cross-index for cross-group pairwise comparisons; DotPlotter-compatible
`PafRecord`	`rusty_dot.paf_io`	Single PAF alignment record
`PafAlignment`	`rusty_dot.paf_io`	Collection of PAF records with reordering utilities; DotPlotter-compatible

Function	Module	Description
`py_read_fasta`	`rusty_dot`	Read a FASTA or gzipped FASTA file
`py_build_kmer_set`	`rusty_dot`	Build the k-mer set for a sequence
`py_find_kmer_coords`	`rusty_dot`	Find k-mer positions in a sequence via FM-index
`py_merge_runs`	`rusty_dot`	Unified strand-aware merge: forward and both RC patterns
`py_merge_kmer_runs`	`rusty_dot`	Merge forward-strand (`+`) co-linear k-mer hits into blocks
`py_merge_rev_runs`	`rusty_dot`	Merge RC anti-diagonal k-mer hits (standard inverted repeat)
`py_merge_rev_fwd_runs`	`rusty_dot`	Merge RC co-diagonal k-mer hits (both arms same direction)
`py_coords_to_paf`	`rusty_dot`	Convert coordinate tuples to PAF lines
`py_save_index`	`rusty_dot`	Serialise an index collection to disk
`py_load_index`	`rusty_dot`	Load a serialised index from disk
`parse_paf_file`	`rusty_dot.paf_io`	Yield PAF records from a file
`compute_gravity_contigs`	`rusty_dot.paf_io`	Sort contigs by gravity centre