from DAJIN2.core.preprocess import (
    align,
    format_inputs,
    check_caches,
)
from DAJIN2.core.preprocess.call_midsv import call_midsv
from DAJIN2.core.preprocess.extract_knockin_loci import extract_knockin_loci

# from DAJIN2.core.preprocess.extract_mutation_loci import process_mutation_loci
from DAJIN2.core.preprocess.extract_mutation_loci import extract_mutation_loci
from DAJIN2.core.preprocess.get_index_mapping import save_index_mapping
from DAJIN2.core.preprocess.generate_insertion_fasta import generate_insertion_fasta
