from DAJIN2.core.preprocess.alignment.mapping import generate_sam
from DAJIN2.core.preprocess.alignment.midsv_caller import generate_midsv
from DAJIN2.core.preprocess.error_correction.sequence_error_handler import (
    detect_sequence_error_reads,
    replace_midsv_without_sequence_errors,
    split_fastq_by_sequence_error,
)
from DAJIN2.core.preprocess.error_correction.strand_bias_handler import extract_sequence_errors_in_strand_biased_loci
from DAJIN2.core.preprocess.genome_coordinate.genome_fetcher import fetch_chromosome_size, fetch_coordinates
from DAJIN2.core.preprocess.infrastructure.directory_manager import (
    create_report_directories,
    create_temporal_directories,
)
from DAJIN2.core.preprocess.infrastructure.input_formatter import format_inputs
from DAJIN2.core.preprocess.mutation_processing.knockin_handler import extract_knockin_loci
from DAJIN2.core.preprocess.mutation_processing.mutation_extractor import cache_mutation_loci
from DAJIN2.core.preprocess.structural_variants.sv_detector import detect_sv_alleles
