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#<< RGFA::Lines
#<=> RGFA::SegmentInfo
#== RGFA::Line
#== RGFA::CIGAR::Operation
#== RGFA
#== RGFA::SegmentInfo
#add RGFA::Line::Header
#all_connections RGFA::Line::Segment
#all_containments RGFA::Line::Segment
#all_links RGFA::Line::Segment
#all_paths RGFA::Line::Segment
#all_references RGFA::Line::Segment
#apply_copy_number RGFATools::CopyNumber
#apply_copy_numbers RGFATools::CopyNumber
#attribute RGFA::SegmentInfo
#attribute= RGFA::SegmentInfo
#attribute_inverted RGFA::SegmentInfo
#canonical? RGFA::Line::Link
#canonical? RGFA::Line::Containment
#canonicize! RGFA::Line::Link
#circular? RGFA::Line::Path
#circular? RGFA::Line::Link
#circular_same_end? RGFA::Line::Link
#clone RGFA::CIGAR
#clone RGFA
#clone RGFA::Line
#code RGFA::CIGAR::Operation
#compatible? RGFA::Line::Link
#compatible_complement? RGFA::Line::Link
#compatible_direct? RGFA::Line::Link
#complement RGFA::CIGAR
#complement RGFA::Line::Link
#complement! RGFA::Line::Link
#complement? RGFA::Line::Link
#complement_overlap RGFA::Line::Link
#compute_copy_numbers RGFATools::CopyNumber
#compute_subtype RGFA::NumericArray
#connected_components RGFA::Connectivity
#connected_segments RGFA::Segments
#connectivity RGFA::Connectivity
#contained_in RGFA::Containments
#containing RGFA::Containments
#containment RGFA::Containments
#containment! RGFA::Containments
#containments RGFA::Line::Segment
#containments RGFA::Containments
#containments_between RGFA::Containments
#counter RGFA::Logger::ProgressData
#coverage RGFA::Line::Segment
#coverage! RGFA::Line::Segment
#cut_link? RGFA::Connectivity
#cut_segment? RGFA::Connectivity
#datatype RGFA::FieldArray
#default_gfa_datatype Fixnum
#default_gfa_datatype RGFA::FieldWriter
#default_gfa_datatype RGFA::NumericArray
#default_gfa_datatype Array
#default_gfa_datatype RGFA::ByteArray
#default_gfa_datatype Float
#default_gfa_datatype RGFA::FieldArray
#default_gfa_datatype Hash
#delete RGFA::Line
#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
#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? RGFA::Line::Link
#eql_optional? RGFA::Line::Link
#field_to_s RGFA::Line
#fieldnames RGFA::Line
#from_end RGFA::Line::Link
from_file RGFA
#from_name RGFA::Line::Link
#from_name RGFA::Line::Containment
from_string RGFA::CIGAR
#get RGFA::Line
#get! RGFA::Line
#get_datatype RGFA::Line
#hash RGFA::Line::Link
#header RGFA::Headers
#headers RGFA::Headers
#info RGFA
#initialize RGFA::CIGAR::Operation
#initialize RGFA::FieldArray
#initialize RGFA::Line
#initialize RGFA
#initialize RGFA::Logger
integer_type RGFA::NumericArray
invert RGFA::SegmentInfo
#invert_attribute RGFA::SegmentInfo
#lastpart RGFA::Logger::ProgressData
#len RGFA::CIGAR::Operation
#length RGFA::Line::Segment
#length! RGFA::Line::Segment
#linear? RGFA::Line::Path
#linear_path RGFA::LinearPaths
#linear_paths RGFA::LinearPaths
#link RGFA::Links
#link! RGFA::Links
#link_from_to RGFA::Links
#link_from_to! RGFA::Links
#links RGFA::Line::Path
#links RGFA::Links
#links RGFA::Line::Segment
#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 RGFA::Line::Header
#merge_linear_path RGFA::LinearPaths
#merge_linear_path RGFATools::LinearPaths
#merge_linear_paths RGFA::LinearPaths
#method_missing RGFA::Line
#multiply RGFA::Multiplication
#multiply_extended RGFATools::Multiplication
#multiply_with_rgfatools RGFATools::Multiplication
#n_dead_ends RGFA
#name RGFA::SegmentInfo
#neighbours RGFA::Links
#optional_fieldnames RGFA::Line
#oriented_from RGFA::Line::Containment
#oriented_from RGFA::Line::Link
#oriented_to RGFA::Line::Containment
#oriented_to RGFA::Line::Link
#other RGFA::Line::Link
#other_end RGFA::Line::Link
#parse_gfa_field RGFA::FieldParser
#parse_gfa_optfield RGFA::FieldParser
#partsize RGFA::Logger::ProgressData
#path RGFA::Paths
#path! RGFA::Paths
#path_names RGFA
#paths RGFA::Paths
#paths RGFA::Line::Link
#paths RGFA::Line::Segment
#paths_with RGFA::Paths
#progress_end RGFA::Logger
#progress_init RGFA::Logger
#progress_log RGFA::LoggerSupport
#progress_log RGFA::Logger
#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
#rc RGFA::Sequence
#read_file RGFA
#real! RGFA::Line
#record_type RGFA::Line
#remove_dead_ends RGFATools::Artifacts
#remove_p_bubble RGFATools::PBubbles
#remove_p_bubbles 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_fieldnames RGFA::Line
#required_links RGFA::Line::Path
#respond_to? RGFA::Line
#reverse RGFA::SegmentEndsPath
#rgfa_field_array? Array
#rm RGFA::Lines
#rpos RGFA::Line::Containment
#same? RGFA::Line::Link
#segment RGFA::SegmentInfo
#segment RGFA::Segments
#segment! RGFA::Segments
#segment= RGFA::SegmentInfo
#segment_connected_component RGFA::Connectivity
#segment_ends_s RGFA::Line::Link
#segment_names RGFA
#segments RGFA::Segments
#set RGFA::Line
#set_count_unit_length RGFATools::CopyNumber
#set_datatype RGFA::Line
#set_default_count_tag RGFATools::CopyNumber
#split RGFA::Line::Header
#split_connected_components RGFA::Connectivity
#starttime RGFA::Logger::ProgressData
#strlen RGFA::Logger::ProgressData
subclass RGFA::Line
#tags RGFA::Line::Header
#tags RGFA::Line
#to_a RGFA::Line
#to_byte_array Array
#to_byte_array RGFA::ByteArray
#to_byte_array String
#to_cigar String
#to_cigar Array
#to_cigar RGFA::CIGAR
#to_cigar_operation Array
#to_cigar_operation RGFA::CIGAR::Operation
#to_end RGFA::Line::Link
#to_file RGFA
#to_gfa_field RGFA::FieldArray
#to_gfa_field RGFA::FieldWriter
#to_gfa_field Hash
#to_gfa_field RGFA::Line::Segment
#to_gfa_field Array
#to_gfa_optfield RGFA::FieldWriter
#to_name RGFA::Line::Link
#to_name RGFA::Line::Containment
#to_numeric_array RGFA::NumericArray
#to_numeric_array String
#to_numeric_array Array
#to_oriented_segment Array
#to_rgfa String
#to_rgfa Array
#to_rgfa RGFA
#to_rgfa_field_array Array
#to_rgfa_line Array
#to_rgfa_line String
#to_rgfa_line RGFA::Line
#to_s RGFA::ByteArray
#to_s RGFA::NumericArray
#to_s RGFA::CIGAR::Operation
#to_s RGFA::CIGAR
#to_s RGFA::Line
#to_s RGFA
#to_s RGFA::SegmentInfo
#to_s RGFA::Line::Segment
#to_segment_end Array
#to_sym RGFA::Line::Path
#to_sym RGFA::Line::Segment
#to_sym RGFA::SegmentInfo
#total RGFA::Logger::ProgressData
#turn_off_validations RGFA
#unconnect_segments RGFA::Segments
#undef_overlaps? RGFA::Line::Path
#units RGFA::Logger::ProgressData
#validate RGFA
#validate! RGFA::ByteArray
#validate! RGFA::CIGAR::Operation
#validate! RGFA::CIGAR
#validate! RGFA::Line
#validate! RGFA
#validate! RGFA::NumericArray
#validate! RGFA::SegmentInfo
#validate_field! RGFA::Line
#validate_gfa_field! RGFA::FieldArray
#validate_gfa_field! Fixnum
#validate_gfa_field! RGFA::ByteArray
#validate_gfa_field! Array
#validate_gfa_field! RGFA::CIGAR
#validate_gfa_field! Symbol
#validate_gfa_field! Object
#validate_gfa_field! RGFA::FieldValidator
#validate_gfa_field! Hash
#validate_gfa_field! RGFA::NumericArray
#validate_gfa_field! Float
#validate_gfa_field! RGFA::Line::Segment
#validate_length! RGFA::Line::Segment
#validate_segment_name! RGFA::FieldValidator
#virtual? RGFA::Line