Method List
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#adj_read_bases Cheripic::Pileup
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#analyse_pileups Cheripic::Variants
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#argument_parser Cheripic::Cmd
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#assembly Cheripic::Variants
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base_quality Cheripic::Options
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#bases_hash Cheripic::Pileup
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#bfr_adj Cheripic::Bfr
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bfr_adjust Cheripic::Options
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#bfr_cutoff Cheripic::Variants
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#bfr_frags Cheripic::Variants
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#bfr_score Cheripic::Contig
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#bg_bulk Cheripic::ContigPileups
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#bg_parent Cheripic::ContigPileups
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#bulks_compared Cheripic::ContigPileups
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calc_fraction Cheripic::Bfr
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calculate_bfr Cheripic::Bfr
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#capture_command Cheripic::Variants
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#categorise_pos Cheripic::ContigPileups
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#check_arguments Cheripic::Cmd
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#check_input_entry Cheripic::Cmd
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#check_input_files Cheripic::Cmd
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#check_input_types Cheripic::Cmd
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#check_log_level Cheripic::Cmd
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#check_output Cheripic::Cmd
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#compare_pileup Cheripic::ContigPileups
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#compare_pileups Cheripic::Variants
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#compare_var_type Cheripic::ContigPileups
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#convert_boolean_strings Cheripic::Cmd
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#count_indel_bases Cheripic::Pileup
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cross_type Cheripic::Options
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current_values Cheripic::Options
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defaults Cheripic::Options
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#extract_bam_pileup Cheripic::Variants
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#extract_pileup Cheripic::Variants
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#extract_vars Cheripic::Implementer
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#extract_vcfs Cheripic::Variants
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#fetch_seq Cheripic::Regions
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#filter_contigs Cheripic::Variants
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filtering Cheripic::Vcf
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#geom_mean Cheripic::Contig
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get_allele_depth Cheripic::Vcf
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get_allele_freq Cheripic::Vcf
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get_bfr Cheripic::Bfr
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#get_cutoff Cheripic::Variants
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#get_id_len Cheripic::Regions
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get_vars Cheripic::Vcf
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#has_run Cheripic::Implementer
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#help_message Cheripic::Cmd
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#hemi_num Cheripic::Contig
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#hemi_pos Cheripic::Contig
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#hemisnps_in_parent Cheripic::ContigPileups
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#hm_num Cheripic::Contig
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#hm_pos Cheripic::Contig
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#hme_score Cheripic::Contig
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hmes_adjust Cheripic::Options
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#hmes_frags Cheripic::Variants
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#ht_num Cheripic::Contig
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#ht_pos Cheripic::Contig
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hthigh Cheripic::Options
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htlow Cheripic::Options
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#id Cheripic::Contig
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#id Cheripic::ContigPileups
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#id_len Cheripic::Regions
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ignore_reference_n Cheripic::Options
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include_low_hmes Cheripic::Options
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#initialize Cheripic::ContigPileups
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#initialize Cheripic::Implementer
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#initialize Cheripic::Variants
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#initialize Cheripic::Pileup
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#initialize Cheripic::Contig
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#initialize Cheripic::Cmd
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#initialize Cheripic::Regions
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#is_var Cheripic::Pileup
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#length Cheripic::Contig
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mapping_quality Cheripic::Options
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#masked_regions Cheripic::ContigPileups
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max_d_multiple Cheripic::Options
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maxdepth Cheripic::Options
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maxdepth= Cheripic::Options
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#mean_depth Cheripic::Contig
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min_indel_count_support Cheripic::Options
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min_non_ref_count Cheripic::Options
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mindepth Cheripic::Options
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#mut_bulk Cheripic::ContigPileups
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#mut_parent Cheripic::ContigPileups
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noise Cheripic::Options
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#non_ref_count Cheripic::Pileup
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#non_ref_ratio Cheripic::Pileup
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#options Cheripic::Implementer
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#options Cheripic::Cmd
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#parent_hemi Cheripic::ContigPileups
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#parse_arguments Cheripic::Cmd
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#pileups Cheripic::Variants
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#pileups_analyzed Cheripic::Variants
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polyploidy Cheripic::Options
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#print_examples Cheripic::Cmd
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#process_variants Cheripic::Implementer
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#reference_db Cheripic::Regions
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#run Cheripic::Implementer
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#run Cheripic::Cmd
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#sd_depth Cheripic::Contig
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sel_seq_len Cheripic::Options
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#select_contigs Cheripic::Variants
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#set_max_depth Cheripic::Variants
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#store_pileup_info Cheripic::Variants
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#store_repeat_regions Cheripic::Variants
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to_pileup Cheripic::Vcf
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update Cheripic::Options
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use_all_contigs Cheripic::Options
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#var_base_frac Cheripic::Pileup
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#var_mode Cheripic::ContigPileups
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#var_mode_fraction Cheripic::ContigPileups
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#variants Cheripic::Implementer
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#verify_bg_bulk_pileup Cheripic::Variants