AlignmentConfig

class panorama.alignment.align.AlignmentConfig(ALIGN_FORMAT=None, ALIGN_COLUMNS=None, DEFAULT_IDENTITY=0.8, DEFAULT_COVERAGE=0.8, DEFAULT_COV_MODE=0, DEFAULT_THREADS=1, INTER_PANGENOMES_OUTPUT='inter_pangenomes.tsv', ALL_AGAINST_ALL_OUTPUT='all_against_all.tsv')

Bases: object

Configuration constants for alignment operations.

ALIGN_COLUMNS: List[str] | None = None

ALIGN_FORMAT: List[str] | None = None

ALL_AGAINST_ALL_OUTPUT: str = 'all_against_all.tsv'

DEFAULT_COVERAGE: float = 0.8

DEFAULT_COV_MODE: int = 0

DEFAULT_IDENTITY: float = 0.8

DEFAULT_THREADS: int = 1

INTER_PANGENOMES_OUTPUT: str = 'inter_pangenomes.tsv'