Table of Contents - cheripic-1.2.7 Documentation
Classes and Modules
- Cheripic
- Cheripic::Bfr
- Cheripic::BfrError
- Cheripic::CheripicArgError
- Cheripic::CheripicError
- Cheripic::CheripicIOError
- Cheripic::Cmd
- Cheripic::Contig
- Cheripic::ContigError
- Cheripic::ContigPileups
- Cheripic::ContigPileupsError
- Cheripic::Implementer
- Cheripic::ImplementerError
- Cheripic::Options
- Cheripic::Pileup
- Cheripic::PileupError
- Cheripic::Regions
- Cheripic::RegionsError
- Cheripic::Variants
- Cheripic::VariantsError
- Cheripic::Vcf
- Cheripic::VcfError
Methods
- ::base_quality — Cheripic::Options
- ::bfr_adjust — Cheripic::Options
- ::calc_fraction — Cheripic::Bfr
- ::calculate_bfr — Cheripic::Bfr
- ::cross_type — Cheripic::Options
- ::current_values — Cheripic::Options
- ::defaults — Cheripic::Options
- ::filtering — Cheripic::Vcf
- ::get_allele_depth — Cheripic::Vcf
- ::get_allele_freq — Cheripic::Vcf
- ::get_bfr — Cheripic::Bfr
- ::get_vars — Cheripic::Vcf
- ::hmes_adjust — Cheripic::Options
- ::hthigh — Cheripic::Options
- ::htlow — Cheripic::Options
- ::ignore_reference_n — Cheripic::Options
- ::include_low_hmes — Cheripic::Options
- ::mapping_quality — Cheripic::Options
- ::max_d_multiple — Cheripic::Options
- ::maxdepth — Cheripic::Options
- ::maxdepth= — Cheripic::Options
- ::min_indel_count_support — Cheripic::Options
- ::min_non_ref_count — Cheripic::Options
- ::mindepth — Cheripic::Options
- ::new — Cheripic::Cmd
- ::new — Cheripic::Contig
- ::new — Cheripic::ContigPileups
- ::new — Cheripic::Implementer
- ::new — Cheripic::Pileup
- ::new — Cheripic::Regions
- ::new — Cheripic::Variants
- ::noise — Cheripic::Options
- ::polyploidy — Cheripic::Options
- ::sel_seq_len — Cheripic::Options
- ::subtract — Cheripic::Vcf
- ::to_pileup — Cheripic::Vcf
- ::update — Cheripic::Options
- ::use_all_contigs — Cheripic::Options
- #adj_read_bases — Cheripic::Pileup
- #analyse_pileups — Cheripic::Variants
- #argument_parser — Cheripic::Cmd
- #bases_hash — Cheripic::Pileup
- #bfr_cutoff — Cheripic::Variants
- #bfr_frags — Cheripic::Variants
- #bfr_score — Cheripic::Contig
- #bulks_compared — Cheripic::ContigPileups
- #capture_command — Cheripic::Variants
- #categorise_pos — Cheripic::ContigPileups
- #check_arguments — Cheripic::Cmd
- #check_input_entry — Cheripic::Cmd
- #check_input_files — Cheripic::Cmd
- #check_input_types — Cheripic::Cmd
- #check_log_level — Cheripic::Cmd
- #check_output — Cheripic::Cmd
- #compare_pileup — Cheripic::ContigPileups
- #compare_pileups — Cheripic::Variants
- #compare_var_type — Cheripic::ContigPileups
- #convert_boolean_strings — Cheripic::Cmd
- #count_indel_bases — Cheripic::Pileup
- #extract_bam_pileup — Cheripic::Variants
- #extract_pileup — Cheripic::Variants
- #extract_vars — Cheripic::Implementer
- #extract_vcfs — Cheripic::Variants
- #fetch_seq — Cheripic::Regions
- #file_exist? — Cheripic::Cmd
- #filter_contigs — Cheripic::Variants
- #geom_mean — Cheripic::Contig
- #get_cutoff — Cheripic::Variants
- #get_id_len — Cheripic::Regions
- #help_message — Cheripic::Cmd
- #hemi_num — Cheripic::Contig
- #hemisnps_in_parent — Cheripic::ContigPileups
- #hm_num — Cheripic::Contig
- #hme_score — Cheripic::Contig
- #hmes_frags — Cheripic::Variants
- #ht_num — Cheripic::Contig
- #indel_non_ref_count — Cheripic::Pileup
- #indels_to_hash — Cheripic::Pileup
- #is_var — Cheripic::Pileup
- #non_ref_count — Cheripic::Pileup
- #non_ref_ratio — Cheripic::Pileup
- #parse_arguments — Cheripic::Cmd
- #print_examples — Cheripic::Cmd
- #process_variants — Cheripic::Implementer
- #run — Cheripic::Cmd
- #run — Cheripic::Implementer
- #select_contigs — Cheripic::Variants
- #send_file_to_extract — Cheripic::Variants
- #set_max_depth — Cheripic::Variants
- #snp_base_hash — Cheripic::Pileup
- #store_pileup_info — Cheripic::Variants
- #store_repeat_regions — Cheripic::Variants
- #var_base_frac — Cheripic::Pileup
- #var_mode — Cheripic::ContigPileups
- #var_mode_fraction — Cheripic::ContigPileups
- #verify_bg_bulk_pileup — Cheripic::Variants