List of all items

Structs

• FULL_VERSION
• cli::AddNucleosomeOptions
• cli::BenchmarkOptions
• cli::CallPeaksOptions
• cli::CenterOptions
• cli::ClearKineticsOptions
• cli::Cli
• cli::CompletionOptions
• cli::ConvertTagsOptions
• cli::DddaToM6aOptions
• cli::DecoratorOptions
• cli::ExtractOptions
• cli::FiberHmmOptions
• cli::FiberHmmParameters
• cli::FireOptions
• cli::FootprintOptions
• cli::GlobalOpts
• cli::MockFireOptions
• cli::NucleosomeParameters
• cli::PansnParameters
• cli::PgInjectOptions
• cli::PgLiftOptions
• cli::PgPansnOptions
• cli::PileupOptions
• cli::PredictM6AOptions
• cli::QcOpts
• cli::StripBasemodsOptions
• cli::ValidateOptions
• fiber::FiberseqData
• fiber::FiberseqRecords
• m6a_burn::BurnModels
• m6a_burn::revio::Model
• m6a_burn::revio::ModelRecord
• m6a_burn::revio::ModelRecordItem
• m6a_burn::three_two::Model
• m6a_burn::three_two::ModelRecord
• m6a_burn::three_two::ModelRecordItem
• m6a_burn::two_two::Model
• m6a_burn::two_two::ModelRecord
• m6a_burn::two_two::ModelRecordItem
• m6a_burn::two_zero::Model
• m6a_burn::two_zero::ModelRecord
• m6a_burn::two_zero::ModelRecordItem
• subcommands::call_peaks::FdrEntry
• subcommands::call_peaks::IncrementalFdrBuilder
• subcommands::call_peaks::PileupRecord
• subcommands::center::CenterPosition
• subcommands::center::CenteredFiberData
• subcommands::decorator::Decorator
• subcommands::extract::FiberOut
• subcommands::footprint::Footprint
• subcommands::footprint::FootprintYaml
• subcommands::footprint::ReferenceMotif
• subcommands::pileup::FiberseqPileup
• subcommands::pileup::FiberseqPileupOptions
• subcommands::pileup::FireElement
• subcommands::pileup::FireRow
• subcommands::pileup::FireTrack
• subcommands::pileup::FireTrackOptions
• subcommands::pileup::ShuffledFibers
• subcommands::predict_m6a::PrecisionTable
• subcommands::predict_m6a::PredictOptions
• subcommands::qc::M6aPerMsp
• subcommands::qc::QcStats
• utils::bamannotations::AnnotationTypeView
• utils::bio_io::BamChunk
• utils::bio_io::BedRecord
• utils::fibertig::FiberTig
• utils::fire::FireFeats
• utils::fire::FireFeatsInRange
• utils::fire::FireFeatsInRangeBuilder
• utils::fire::MapPrecisionValues
• utils::fire::PrecisionTable
• utils::ftexpression::ParsedExpr
• utils::input_bam::FiberFilters
• utils::input_bam::InputBam

Enums

• cli::Commands
• utils::bio_io::PbChem
• utils::fire::FireFeatsInRangeBuilderError
• utils::platform::SeqPlatform

Functions

• cli::make_cli_app
• cli::make_cli_parse
• cli::print_completions
• join_by_str
• join_by_str_option
• join_by_str_option_can_skip
• region_parser
• subcommands::add_nucleosomes::add_nucleosomes_to_bam
• subcommands::benchmark::run_benchmark
• subcommands::call_peaks::call_peaks
• subcommands::call_peaks::chrom_names_and_lengths
• subcommands::call_peaks::fdr_table
• subcommands::call_peaks::lookup_fdr
• subcommands::call_peaks::read_fdr_table
• subcommands::call_peaks::reciprocal_overlap_raw
• subcommands::call_peaks::run_call_peaks
• subcommands::call_peaks::write_fdr_table
• subcommands::center::center
• subcommands::center::center_fiberdata
• subcommands::center::read_center_positions
• subcommands::clear_kinetics::clear_kinetics
• subcommands::convert_tags::convert_tags
• subcommands::ddda_to_m6a::ddda_to_m6a
• subcommands::ddda_to_m6a::ddda_to_m6a_record
• subcommands::decorator::bed12_from_fiber
• subcommands::decorator::decorator_from_bam
• subcommands::decorator::fire_decorators
• subcommands::decorator::get_decorators_from_bam
• subcommands::decorator::get_fire_color
• subcommands::decorator::pos_to_string
• subcommands::extract::extract_contained
• subcommands::extract::process_bam_chunk
• subcommands::fiber_hmm::run_fiber_hmm
• subcommands::fire::add_fire_to_bam
• subcommands::fire::add_fire_to_rec
• subcommands::fire::fire_to_bed9
• subcommands::footprint::define_footprint
• subcommands::footprint::start_finding_footprints
• subcommands::mock_fire::run_mock_fire
• subcommands::pg_inject::run_pg_inject
• subcommands::pg_lift::run_pg_lift
• subcommands::pg_pansn::apply_pansn_transformations
• subcommands::pg_pansn::copy_header_from_bam
• subcommands::pg_pansn::haplotype::add_haplotype_tag
• subcommands::pg_pansn::haplotype::build_haplotype_map
• subcommands::pg_pansn::haplotype::determine_haplotype
• subcommands::pg_pansn::run_pg_pansn
• subcommands::pg_pansn::strip_pansn_from_contig_name
• subcommands::pileup::pileup_track
• subcommands::pileup::split_fetch_definition
• subcommands::predict_m6a::hot_one_dna
• subcommands::predict_m6a::read_bam_into_fiberdata
• subcommands::qc::run_qc
• subcommands::strip_basemods::strip_base_mods
• subcommands::validate::eprintln_green
• subcommands::validate::eprintln_red
• subcommands::validate::validate_fiberseq_bam
• unzip_to_vectors
• utils::acf::acf
• utils::acf::acf_par
• utils::bamannotations::primary_qual
• utils::basemods::canonical_basemod
• utils::basemods::canonical_header
• utils::basemods::is_basemod_type
• utils::bio_io::bam_header_to_string
• utils::bio_io::bam_reader
• utils::bio_io::buffer_from
• utils::bio_io::convert_seq_uppercase
• utils::bio_io::find_pb_polymerase
• utils::bio_io::get_f32_tag
• utils::bio_io::get_pb_u16_tag_as_u8
• utils::bio_io::get_u32_tag
• utils::bio_io::get_u8_tag
• utils::bio_io::header_from_hashmap
• utils::bio_io::no_length_progress_bar
• utils::bio_io::program_bam_writer
• utils::bio_io::program_bam_writer_from_header
• utils::bio_io::read_bed_regions
• utils::bio_io::write_record
• utils::bio_io::write_to_file
• utils::bio_io::writer
• utils::fire::get_bins
• utils::fire::get_model
• utils::ftexpression::apply_filter_fsd
• utils::ftexpression::parse_filter
• utils::ftexpression::parse_filter_all
• utils::ma_io::add_fire_annotations
• utils::ma_io::add_msp_annotations
• utils::ma_io::add_nuc_annotations
• utils::ma_io::build_annotations
• utils::ma_io::build_nuc_msp_annotations
• utils::ma_io::extract_fire_arrays
• utils::ma_io::extract_nuc_msp_arrays
• utils::ma_io::read_annotations
• utils::ma_io::read_record
• utils::ma_io::write_record
• utils::ma_io::write_record_with_basemods
• utils::nucleosome::add_nucleosomes_to_annotations
• utils::nucleosome::check_nucleosomes
• utils::nucleosome::d_segment_nucleosomes
• utils::nucleosome::filter_for_end
• utils::nucleosome::find_msps
• utils::nucleosome::find_nucleosomes
• utils::panspec::add_pan_spec_header
• utils::panspec::strip_pan_spec_header
• utils::platform::platform_from_aux
• utils::platform::platform_from_qname
• utils::platform::platform_from_record

Type Aliases

• m6a_burn::BurnDevice

Statics

• cli::ALLOWED_SKIPS
• cli::COMBO_NUC_LEN
• cli::DIST_FROM_END
• cli::MIN_DIST_ADDED
• cli::NUC_LEN
• subcommands::predict_m6a::SEMI_JSON_2_0
• subcommands::predict_m6a::SEMI_JSON_2_2
• subcommands::predict_m6a::SEMI_JSON_3_2
• subcommands::predict_m6a::SEMI_JSON_REVIO
• utils::fire::FIRE_CONF_JSON
• utils::fire::FIRE_MODEL
• utils::input_bam::MIN_ML_SCORE

Constants

• CPG_COLOR
• FIRE_COLORS
• LINKER_COLOR
• M6A_COLOR
• NUC_COLOR
• VERSION
• subcommands::predict_m6a::LAYERS
• subcommands::predict_m6a::MIN_F32_PRED
• subcommands::predict_m6a::WINDOW
• utils::basemods::CPG_TYPE
• utils::basemods::M6A_TYPE
• utils::fibertig::FIBERTIG_TYPE
• utils::ma_io::FIRE_TYPE
• utils::ma_io::LEGACY_READ_TAGS
• utils::ma_io::MSP_TYPE
• utils::ma_io::NUC_TYPE