from DAJIN2.core.preprocess.cache_checker import exists_cached_genome, exists_cached_hash
from DAJIN2.core.preprocess.directory_manager import create_report_directories, create_temporal_directories
from DAJIN2.core.preprocess.genome_fetcher import fetch_chromosome_size, fetch_coordinates
from DAJIN2.core.preprocess.input_formatter import format_inputs
from DAJIN2.core.preprocess.insertion_detector import detect_insertions
from DAJIN2.core.preprocess.inversion_detector import detect_inversions
from DAJIN2.core.preprocess.knockin_handler import extract_knockin_loci
from DAJIN2.core.preprocess.mapping import generate_sam
from DAJIN2.core.preprocess.midsv_caller import generate_midsv
from DAJIN2.core.preprocess.mutation_extractor import cache_mutation_loci
