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#adj_read_bases Pileup
#analyse_pileups Cheripic::Variants
#argument_parser Cheripic::Cmd
#assembly Cheripic::Variants
#bases_hash Pileup
#bfr_adj Cheripic::Bfr
#bfr_cutoff Cheripic::Variants
#bfr_frags Cheripic::Variants
#bfr_score Cheripic::Contig
#bg_bulk Cheripic::ContigPileups
#bg_bulk_var Cheripic::ContigPileups
#bg_parent Cheripic::ContigPileups
#bulks_compared Cheripic::ContigPileups
calc_fraction Cheripic::Bfr
calculate_bfr Cheripic::Bfr
#categorise_pos Cheripic::ContigPileups
#check_arguments Cheripic::Cmd
#check_input_files Cheripic::Cmd
#check_log_level Cheripic::Cmd
#check_output_dir Cheripic::Cmd
#compare_pileup Cheripic::ContigPileups
#compare_pileups Cheripic::Variants
#compare_var_type Cheripic::ContigPileups
#count_indel_bases Pileup
#defaults Pileup
#extract_pileup Cheripic::Variants
#extract_vars Cheripic::Implementer
#fetch_seq Cheripic::Regions
#filter_contigs Cheripic::Variants
#geom_mean Cheripic::Contig
get_bfr Cheripic::Bfr
#get_cutoff Cheripic::Variants
#get_id_len Cheripic::Regions
#has_run Cheripic::Variants
#help_message Cheripic::Cmd
#hemi_num Cheripic::Contig
#hemi_pos Cheripic::Contig
#hemisnps_in_parent Cheripic::ContigPileups
#hm_num Cheripic::Contig
#hm_pos Cheripic::Contig
#hme_score Cheripic::Contig
#hmes_frags Cheripic::Variants
#ht_num Cheripic::Contig
#ht_pos Cheripic::Contig
#id Cheripic::ContigPileups
#id Cheripic::Contig
#id_len Cheripic::Regions
#initialize Cheripic::ContigPileups
#initialize Pileup
#initialize Cheripic::Contig
#initialize Cheripic::Implementer
#initialize Cheripic::Cmd
#initialize Cheripic::Regions
#initialize Cheripic::Variants
#is_var Pileup
#length Cheripic::Contig
#mut_bulk Cheripic::ContigPileups
#mut_parent Cheripic::ContigPileups
#non_ref_count Pileup
#non_ref_ratio Pileup
#options Cheripic::Cmd
#options Cheripic::Implementer
params Cheripic::Options
#parent_hemi Cheripic::ContigPileups
#parse_arguments Cheripic::Cmd
#pileups Cheripic::Variants
#print_examples Cheripic::Cmd
#process_variants Cheripic::Implementer
#reference_db Cheripic::Regions
#run Cheripic::Implementer
#run Cheripic::Cmd
#select_contigs Cheripic::Variants
#set_defaults Pileup
update Cheripic::Options
#var_base_frac Pileup
#var_mode Pileup
#var_mode Cheripic::ContigPileups
#variants Cheripic::Implementer
#verify_bg_bulk_pileup Cheripic::Variants