kaptive.core¶

Core data structures, container protocols, and computational engines.

The kaptive.core sub-package provides high-performance data structures, interval operations, k-mer indexing algorithms, and pairwise sequence alignment routines underlying Kaptive's serotyping and BGC prediction functionality.

Modules:

• alignment –

  CIGAR parsing, alignment models, and batched alignment containers (e.g., Alignments, Alignment, Cigars).

• collections –

  Protocol base classes for Structure-of-Arrays containers (e.g., BatchedContainer, RaggedArrayContainer).

• genome –

  Genome assembly parsing and FASTA sequence iteration (e.g., GenomeAssembly, FastaReader).

• interval –

  Genomic interval representations, clustering, and overlap resolution (e.g., Interval, Intervals, Strand).

• kmers –

  MinHash and Randstrobe k-mer indexing and matching engines (e.g., RandstrobeIndex, FracMinHashIndex, Seeds).

• pairwise –

  Batched dynamic programming pairwise alignment engines (e.g., PairwiseAligner, PairwiseAlignments).

• seq –

  Sequence storage, vectorised translation, and sequence record metadata (e.g., Sequences, SeqRecord).