List of all items
Structs
- FULL_VERSION
- cli::AddNucleosomeOptions
- cli::CenterOptions
- cli::ClearKineticsOptions
- cli::Cli
- cli::CompletionOptions
- cli::DddaToM6aOptions
- cli::DecoratorOptions
- cli::ExtractOptions
- cli::FireOptions
- cli::FootprintOptions
- cli::GlobalOpts
- cli::NucleosomeParameters
- cli::PileupOptions
- cli::PredictM6AOptions
- cli::QcOpts
- cli::StripBasemodsOptions
- 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::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::FireRow
- subcommands::pileup::FireTrack
- subcommands::pileup::ShuffledFibers
- subcommands::predict_m6a::PrecisionTable
- subcommands::predict_m6a::PredictOptions
- subcommands::qc::M6aPerMsp
- subcommands::qc::QcStats
- utils::bamranges::Ranges
- utils::bamranges::RangesIterator
- utils::basemods::BaseMod
- utils::basemods::BaseMods
- utils::bio_io::BamChunk
- 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
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::center::center
- subcommands::center::center_fiberdata
- subcommands::center::read_center_positions
- subcommands::clear_kinetics::clear_kinetics
- 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::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::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
- unzip_to_vectors
- utils::acf::acf
- utils::acf::acf_par
- utils::bamlift::is_sorted
- utils::bamlift::lift_query_positions
- utils::bamlift::lift_query_positions_exact
- utils::bamlift::lift_query_range
- utils::bamlift::lift_query_range_exact
- utils::bamlift::lift_reference_positions
- utils::bamlift::lift_reference_positions_exact
- utils::bamlift::lift_reference_range_exact
- utils::bamlift::merge_two_lists
- utils::bamlift::merge_two_lists_with_qual
- utils::bio_io::bam_reader
- utils::bio_io::buffer_from
- 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::no_length_progress_bar
- utils::bio_io::program_bam_writer
- utils::bio_io::program_bam_writer_from_header
- 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::apply_filter_to_range
- utils::ftexpression::parse_filter
- utils::ftexpression::parse_filter_all
- utils::nucleosome::add_nucleosomes_to_record
- utils::nucleosome::check_nucleosomes
- utils::nucleosome::d_segment_nucleosomes
- utils::nucleosome::filter_for_end
- utils::nucleosome::find_msps
- utils::nucleosome::find_nucleosomes
Type Aliases
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