Table of Contents - rgfa-1.3.1 Documentation
Classes and Modules
- Array
- Fixnum
- Float
- Hash
- Line::Comment
- Line::Containment
- Line::CustomOptfieldNameError
- Line::DuplicatedOptfieldNameError
- Line::FieldnameError
- Line::Header
- Line::Link
- Line::Path
- Line::PredefinedOptfieldTypeError
- Line::RequiredFieldMissingError
- Line::TagMissingError
- Line::UnknownDatatype
- Line::UnknownRecordTypeError
- Object
- RGFA
- RGFA
- RGFA::ByteArray
- RGFA::ByteArray::FormatError
- RGFA::ByteArray::ValueError
- RGFA::CIGAR
- RGFA::CIGAR::Operation
- RGFA::CIGAR::ValueError
- RGFA::Connectivity
- RGFA::Containments
- RGFA::DuplicatedLabelError
- RGFA::Error
- RGFA::FieldArray
- RGFA::FieldArray::Error
- RGFA::FieldArray::TypeMismatchError
- RGFA::FieldParser
- RGFA::FieldParser::FormatError
- RGFA::FieldParser::UnknownDatatypeError
- RGFA::FieldValidator
- RGFA::FieldWriter
- RGFA::Headers
- RGFA::Line
- RGFA::Line::Path
- RGFA::Line::Path::ListLengthsError
- RGFA::LineMissingError
- RGFA::LinearPaths
- RGFA::Lines
- RGFA::Links
- RGFA::Logger
- RGFA::LoggerSupport
- RGFA::Multiplication
- RGFA::NumericArray
- RGFA::NumericArray::TypeError
- RGFA::NumericArray::ValueError
- RGFA::OrientedSegment
- RGFA::Paths
- RGFA::RGL
- RGFA::RGL::ClassMethods
- RGFA::RGL::InvalidFormatError
- RGFA::RGL::ValueError
- RGFA::SegmentEnd
- RGFA::SegmentEndsPath
- RGFA::SegmentInfo
- RGFA::SegmentInfo::InvalidAttributeError
- RGFA::SegmentInfo::InvalidSizeError
- RGFA::Segments
- RGFA::Sequence
- RGFATools
- RGFATools::Artifacts
- RGFATools::CopyNumber
- RGFATools::InvertibleSegments
- RGFATools::LinearPaths
- RGFATools::Multiplication
- RGFATools::PBubbles
- RGFATools::SuperfluousLinks
- RGL
- RGL::Graph
- Segment
- Segment::InconsistentLengthError
- Segment::UndefinedLengthError
- String
- Symbol
Methods
- ::from_file — RGFA
- ::from_string — RGFA::CIGAR
- ::included — RGFA::RGL
- ::included — RGFATools
- ::integer_type — RGFA::NumericArray
- ::invert — RGFA::SegmentInfo
- ::new — RGFA
- ::new — RGFA::CIGAR::Operation
- ::new — RGFA::FieldArray
- ::new — RGFA::Logger
- ::redefine_methods — RGFATools
- #<< — RGFA::Lines
- #<=> — RGFA::SegmentInfo
- #== — RGFA
- #== — RGFA::CIGAR::Operation
- #== — RGFA::SegmentInfo
- #add — Line::Header
- #add_containment — RGFA::Containments
- #add_header — RGFA::Headers
- #add_link — RGFA::Links
- #add_path — RGFA::Paths
- #add_program_name_to_header — RGFATools
- #add_segment — RGFA::Segments
- #add_segment_if_new — RGFA::RGL::ClassMethods
- #add_segment_to_merged — RGFA::LinearPaths
- #add_segment_to_merged_with_rgfatools — RGFATools::LinearPaths
- #all_connections — Segment
- #all_containments — Segment
- #all_links — Segment
- #all_paths — Segment
- #all_references — Segment
- #annotate_random_orientation — RGFATools::InvertibleSegments
- #apply_copy_number — RGFATools::CopyNumber
- #apply_copy_numbers — RGFATools::CopyNumber
- #attribute — RGFA::SegmentInfo
- #attribute= — RGFA::SegmentInfo
- #attribute_inverted — RGFA::SegmentInfo
- #auto_select_distribute_end — RGFATools::Multiplication
- #canonical? — Line::Containment
- #canonical? — Line::Link
- #canonicize! — Line::Link
- #circular? — Line::Link
- #circular? — Line::Path
- #circular_same_end? — Line::Link
- #clone — RGFA
- #clone — RGFA::CIGAR
- #clone_segment_and_connections — RGFA::Multiplication
- #compatible? — Line::Link
- #compatible_complement? — Line::Link
- #compatible_direct? — Line::Link
- #complement — RGFA::CIGAR
- #complement — Line::Link
- #complement! — Line::Link
- #complement? — Line::Link
- #complement_overlap — Line::Link
- #compute_copy_names — RGFA::Multiplication
- #compute_copy_numbers — RGFATools::CopyNumber
- #compute_subtype — RGFA::NumericArray
- #connected_components — RGFA::Connectivity
- #connected_segments — RGFA::Segments
- #connectivity — RGFA::Connectivity
- #connectivity_symbol — RGFA::Connectivity
- #connectivity_symbols — RGFA::Connectivity
- #contained_in — RGFA::Containments
- #containing — RGFA::Containments
- #containment — RGFA::Containments
- #containment! — RGFA::Containments
- #containments — Segment
- #containments — RGFA::Containments
- #containments_between — RGFA::Containments
- #coverage — Segment
- #coverage! — Segment
- #create_merged_segment — RGFA::LinearPaths
- #cut_link? — RGFA::Connectivity
- #cut_segment? — RGFA::Connectivity
- #default_gfa_datatype — Array
- #default_gfa_datatype — RGFA::ByteArray
- #default_gfa_datatype — RGFA::FieldArray
- #default_gfa_datatype — Hash
- #default_gfa_datatype — RGFA::NumericArray
- #default_gfa_datatype — Float
- #default_gfa_datatype — Fixnum
- #default_gfa_datatype — RGFA::FieldWriter
- #delete_containment — RGFA::Containments
- #delete_headers — RGFA::Headers
- #delete_link — RGFA::Links
- #delete_low_coverage_segments — RGFATools::CopyNumber
- #delete_other_links — RGFA::Links
- #delete_path — RGFA::Paths
- #delete_segment — RGFA::Segments
- #disable_extensions — RGFA
- #disable_progress — RGFA::Logger
- #distribute_links — RGFATools::Multiplication
- #divide_counts — RGFA::Multiplication
- #divide_segment_and_connection_counts — RGFA::Multiplication
- #each_line — RGFA::Lines
- #enable_extensions — RGFA
- #enable_progress — RGFA::Logger
- #enable_progress_logging — RGFA::LoggerSupport
- #enforce_all_mandatory_links — RGFATools::SuperfluousLinks
- #enforce_segment_mandatory_links — RGFATools::SuperfluousLinks
- #eql? — Line::Link
- #eql_optional? — Line::Link
- #from_end — Line::Link
- #from_name — Line::Containment
- #from_name — Line::Link
- #from_rgl — RGFA::RGL::ClassMethods
- #hash — Line::Link
- #header — RGFA::Headers
- #headers — RGFA::Headers
- #info — RGFA
- #init_headers — RGFA
- #invert_attribute — RGFA::SegmentInfo
- #length — Segment
- #length! — Segment
- #lenstats — RGFA
- #linear? — Line::Path
- #linear_path — RGFA::LinearPaths
- #linear_paths — RGFA::LinearPaths
- #lines — RGFA::Lines
- #link — RGFA::Links
- #link! — RGFA::Links
- #link_from_to — RGFA::Links
- #link_from_to! — RGFA::Links
- #link_merged — RGFA::LinearPaths
- #link_targets_for_cmp — RGFATools::InvertibleSegments
- #links — Segment
- #links — Line::Path
- #links — RGFA::Links
- #links_between — RGFA::Links
- #links_from — RGFA::Links
- #links_from_to — RGFA::Links
- #links_of — RGFA::Links
- #links_to — RGFA::Links
- #log — RGFA::Logger
- #merge — Line::Header
- #merge_linear_path — RGFA::LinearPaths
- #merge_linear_paths — RGFA::LinearPaths
- #multiply — RGFA::Multiplication
- #multiply_extended — RGFATools::Multiplication
- #multiply_with_rgfatools — RGFATools::Multiplication
- #n_dead_ends — RGFA
- #name — RGFA::SegmentInfo
- #neighbours — RGFA::Links
- #oriented_from — Line::Containment
- #oriented_from — Line::Link
- #oriented_to — Line::Containment
- #oriented_to — Line::Link
- #other — Line::Link
- #other_end — Line::Link
- #parse_gfa_field — RGFA::FieldParser
- #parse_gfa_optfield — RGFA::FieldParser
- #partitioned_links_of — RGFATools::InvertibleSegments
- #path — RGFA::Paths
- #path! — RGFA::Paths
- #path_names — RGFA
- #paths — Segment
- #paths — Line::Link
- #paths — RGFA::Paths
- #paths_with — RGFA::Paths
- #progress_end — RGFA::Logger
- #progress_init — RGFA::Logger
- #progress_log — RGFA::Logger
- #progress_log — RGFA::LoggerSupport
- #progress_log_end — RGFA::LoggerSupport
- #progress_log_init — RGFA::LoggerSupport
- #push_with_validation — RGFA::FieldArray
- #randomly_orient_invertible — RGFATools::InvertibleSegments
- #randomly_orient_invertibles — RGFATools::InvertibleSegments
- #randomly_orient_proven_invertible_segment — RGFATools::InvertibleSegments
- #rc — RGFA::Sequence
- #read_file — RGFA
- #remove_dead_ends — RGFATools::Artifacts
- #remove_p_bubble — RGFATools::PBubbles
- #remove_p_bubbles — RGFATools::PBubbles
- #remove_proven_p_bubble — RGFATools::PBubbles
- #remove_self_link — RGFATools::SuperfluousLinks
- #remove_self_links — RGFATools::SuperfluousLinks
- #remove_small_components — RGFATools::Artifacts
- #rename — RGFA::Lines
- #require_segments_first_order — RGFA
- #required_links — Line::Path
- #reverse — RGFA::SegmentEndsPath
- #reverse_pos_array — RGFA::LinearPaths
- #reverse_pos_array — RGFATools::LinearPaths
- #reverse_segment_name — RGFA::LinearPaths
- #reverse_segment_name — RGFATools::LinearPaths
- #rgfa_field_array? — Array
- #rm — RGFA::Lines
- #rpos — Line::Containment
- #same? — Line::Link
- #segment — RGFA::SegmentInfo
- #segment — RGFA::Segments
- #segment! — RGFA::Segments
- #segment= — RGFA::SegmentInfo
- #segment_and_segment_name — RGFATools::Multiplication
- #segment_connected_component — RGFA::Connectivity
- #segment_ends_s — Line::Link
- #segment_name_and_orient — RGFA::RGL::ClassMethods
- #segment_names — RGFA
- #segment_same_links_both_ends? — RGFATools::InvertibleSegments
- #segment_signature — RGFATools::InvertibleSegments
- #segments — RGFA::Segments
- #select_distribute_end — RGFATools::Multiplication
- #set_count_unit_length — RGFATools::CopyNumber
- #set_default_count_tag — RGFATools::CopyNumber
- #split — Line::Header
- #split_connected_components — RGFA::Connectivity
- #sum_of_counts — RGFA::LinearPaths
- #tags — Line::Header
- #to_byte_array — String
- #to_byte_array — Array
- #to_byte_array — RGFA::ByteArray
- #to_cigar — String
- #to_cigar — Array
- #to_cigar — RGFA::CIGAR
- #to_cigar_operation — Array
- #to_cigar_operation — RGFA::CIGAR::Operation
- #to_end — Line::Link
- #to_file — RGFA
- #to_gfa_field — Array
- #to_gfa_field — RGFA::FieldArray
- #to_gfa_field — Hash
- #to_gfa_field — Segment
- #to_gfa_field — RGFA::FieldWriter
- #to_gfa_optfield — RGFA::FieldWriter
- #to_name — Line::Containment
- #to_name — Line::Link
- #to_numeric_array — String
- #to_numeric_array — Array
- #to_numeric_array — RGFA::NumericArray
- #to_oriented_segment — Array
- #to_rgfa — RGFA
- #to_rgfa — String
- #to_rgfa — Array
- #to_rgfa — RGL::Graph
- #to_rgfa_field_array — Array
- #to_rgfa_line — String
- #to_rgfa_line — Array
- #to_rgl — RGFA::RGL
- #to_rgl_oriented — RGFA::RGL
- #to_rgl_unoriented — RGFA::RGL
- #to_s — RGFA
- #to_s — RGFA::ByteArray
- #to_s — RGFA::CIGAR
- #to_s — RGFA::CIGAR::Operation
- #to_s — RGFA::NumericArray
- #to_s — Segment
- #to_s — RGFA::SegmentInfo
- #to_segment_end — Array
- #to_segment_info — Array
- #to_sym — Segment
- #to_sym — Line::Path
- #to_sym — RGFA::SegmentInfo
- #traverse_component — RGFA::Connectivity
- #traverse_linear_path — RGFA::LinearPaths
- #turn_off_validations — RGFA
- #unconnect_segments — RGFA::Segments
- #undef_overlaps? — Line::Path
- #validate! — RGFA
- #validate! — RGFA::ByteArray
- #validate! — RGFA::CIGAR
- #validate! — RGFA::CIGAR::Operation
- #validate! — RGFA::NumericArray
- #validate! — RGFA::SegmentInfo
- #validate_gfa_field! — Array
- #validate_gfa_field! — RGFA::ByteArray
- #validate_gfa_field! — RGFA::CIGAR
- #validate_gfa_field! — RGFA::FieldArray
- #validate_gfa_field! — Object
- #validate_gfa_field! — Symbol
- #validate_gfa_field! — Hash
- #validate_gfa_field! — RGFA::NumericArray
- #validate_gfa_field! — Float
- #validate_gfa_field! — Fixnum
- #validate_gfa_field! — Segment
- #validate_gfa_field! — RGFA::FieldValidator
- #validate_length! — Segment
- #validate_lists_size! — Line::Path
- #validate_path_links! — RGFA
- #validate_record_type_specific_info! — Segment
- #validate_record_type_specific_info! — Line::Path
- #validate_segment_name! — RGFA::FieldValidator
- #validate_segment_references! — RGFA