Index

_

__BIN2ASCII_H__ (C macro) _CONVERT (C macro), [1] _field2json (C++ function)

_json2field (C++ function) _json2pb (C++ function) _pb2json (C++ function) _SET_OR_ADD (C macro)

A

add_log (C++ function) Aligner::align (C++ function) Aligner::align_global_banded (C++ function) Aligner::align_global_banded_multi (C++ function) Aligner::align_internal (C++ function) Aligner::align_pinned (C++ function) Aligner::align_pinned_multi (C++ function) Aligner::Aligner (C++ function) Aligner::compute_mapping_quality (C++ function) Aligner::compute_paired_mapping_quality (C++ function) Aligner::create_gssw_graph (C++ function)

Aligner::graph_cigar (C++ function) Aligner::gssw_mapping_to_alignment (C++ function) Aligner::init_mapping_quality (C++ function) Aligner::is_mapping_quality_initialized (C++ function) Aligner::maximum_mapping_quality_approx (C++ function) Aligner::maximum_mapping_quality_exact (C++ function) Aligner::reverse_graph (C++ function) Aligner::score_exact_match (C++ function) Aligner::score_to_unnormalized_likelihood_ln (C++ function) Aligner::unreverse_graph (C++ function) Aligner::unreverse_graph_mapping (C++ function) Aligner::~Aligner (C++ function)

B

b64_decode (C++ function) b64_encode (C++ function) BandedGlobalAligner::align (C++ function) BandedGlobalAligner::AltTracebackStack::AltTracebackStack (C++ function) BandedGlobalAligner::AltTracebackStack::at_next_deflection (C++ function) BandedGlobalAligner::AltTracebackStack::current_traceback_score (C++ function) BandedGlobalAligner::AltTracebackStack::deflect_to_matrix (C++ function), [1] BandedGlobalAligner::AltTracebackStack::Deflection::Deflection (C++ function) BandedGlobalAligner::AltTracebackStack::Deflection::~Deflection (C++ function) BandedGlobalAligner::AltTracebackStack::get_alignment_start (C++ function) BandedGlobalAligner::AltTracebackStack::has_next (C++ function) BandedGlobalAligner::AltTracebackStack::insert_traceback (C++ function) BandedGlobalAligner::AltTracebackStack::next (C++ function) BandedGlobalAligner::AltTracebackStack::propose_deflection (C++ function) BandedGlobalAligner::AltTracebackStack::~AltTracebackStack (C++ function) BandedGlobalAligner::BABuilder::BABuilder (C++ function) BandedGlobalAligner::BABuilder::finalize_alignment (C++ function) BandedGlobalAligner::BABuilder::finish_current_edit (C++ function) BandedGlobalAligner::BABuilder::finish_current_node (C++ function)

BandedGlobalAligner::BABuilder::update_state (C++ function) BandedGlobalAligner::BABuilder::~BABuilder (C++ function) BandedGlobalAligner::BAMatrix::BAMatrix (C++ function) BandedGlobalAligner::BAMatrix::fill_matrix (C++ function) BandedGlobalAligner::BAMatrix::print_band (C++ function) BandedGlobalAligner::BAMatrix::print_full_matrices (C++ function) BandedGlobalAligner::BAMatrix::print_matrix (C++ function) BandedGlobalAligner::BAMatrix::print_rectangularized_bands (C++ function) BandedGlobalAligner::BAMatrix::traceback (C++ function) BandedGlobalAligner::BAMatrix::traceback_internal (C++ function) BandedGlobalAligner::BAMatrix::~BAMatrix (C++ function) BandedGlobalAligner::BandedGlobalAligner (C++ function), [1], [2] BandedGlobalAligner::find_banded_paths (C++ function) BandedGlobalAligner::graph_edge_lists (C++ function) BandedGlobalAligner::path_lengths_to_sinks (C++ function) BandedGlobalAligner::shortest_seq_paths (C++ function) BandedGlobalAligner::topological_sort (C++ function) BandedGlobalAligner::traceback (C++ function) BandedGlobalAligner::~BandedGlobalAligner (C++ function) bin2hex (C++ function)

C

CATCH_CONFIG_RUNNER (C macro)

convert (C++ function), [1]

E

exp_overflow_limit (C++ member)

G

gfak (C++ type) glenn2vcf (C++ type) glenn2vcf::add_alt_allele (C++ function) glenn2vcf::bfs_left (C++ function) glenn2vcf::bfs_right (C++ function) glenn2vcf::bp_length (C++ function) glenn2vcf::call2vcf (C++ function), [1] glenn2vcf::can_write_alleles (C++ function) glenn2vcf::char_to_string (C++ function) glenn2vcf::create_ref_allele (C++ function) glenn2vcf::deletionEdges (C++ member) glenn2vcf::edgeReadSupport (C++ member) glenn2vcf::factorial (C++ function) glenn2vcf::find_bubble (C++ function) glenn2vcf::flip (C++ function) glenn2vcf::gammaln (C++ function) glenn2vcf::get_pileup_line (C++ function) glenn2vcf::IntervalBitfield (C++ class) glenn2vcf::IntervalBitfield::add (C++ function) glenn2vcf::IntervalBitfield::collides (C++ function) glenn2vcf::IntervalBitfield::IntervalBitfield (C++ function) glenn2vcf::IntervalBitfield::used (C++ member) glenn2vcf::knownEdges (C++ member) glenn2vcf::knownNodes (C++ member) glenn2vcf::LOG_ZERO (C++ member)

glenn2vcf::mapping_is_perfect_match (C++ function) glenn2vcf::MAX_ALLELE_LENGTH (C++ member) glenn2vcf::min_support_in_path (C++ function) glenn2vcf::nodeReadSupport (C++ member) glenn2vcf::nodeSources (C++ member) glenn2vcf::operator* (C++ function), [1] glenn2vcf::operator+ (C++ function) glenn2vcf::operator+= (C++ function) glenn2vcf::operator/ (C++ function) glenn2vcf::operator<< (C++ function) glenn2vcf::parse_tsv (C++ function) glenn2vcf::poissonp (C++ function) glenn2vcf::ReferenceIndex (C++ class) glenn2vcf::ReferenceIndex::byId (C++ member) glenn2vcf::ReferenceIndex::byStart (C++ member) glenn2vcf::ReferenceIndex::sequence (C++ member) glenn2vcf::strand_bias (C++ function) glenn2vcf::Support (C++ type) glenn2vcf::support_min (C++ function) glenn2vcf::to_string_ss (C++ function) glenn2vcf::total (C++ function) glenn2vcf::trace_reference_path (C++ function) glenn2vcf::write_vcf_header (C++ function) google (C++ type) google::protobuf (C++ type)

H

help_align (C++ function) help_call (C++ function) help_circularize (C++ function) help_compare (C++ function) help_concat (C++ function) help_construct (C++ function) help_deconstruct (C++ function) help_filter (C++ function) help_find (C++ function) help_genotype (C++ function) help_ids (C++ function) help_index (C++ function) help_join (C++ function) help_kmers (C++ function) help_locify (C++ function) help_map (C++ function)

help_mod (C++ function) help_msga (C++ function) help_paths (C++ function) help_pileup (C++ function) help_scrub (C++ function) help_sim (C++ function) help_simplify (C++ function) help_stats (C++ function) help_surject (C++ function) help_sv (C++ function) help_translate (C++ function) help_validate (C++ function) help_vectorize (C++ function) help_version (C++ function) help_view (C++ function) hex2bin (C++ function)

J

j2pb_error (C++ class) j2pb_error::_error (C++ member) j2pb_error::j2pb_error (C++ function), [1] j2pb_error::what (C++ function) j2pb_error::~j2pb_error (C++ function) json2pb (C++ function), [1], [2], [3] json_autoptr (C++ class) json_autoptr::json_autoptr (C++ function) json_autoptr::ptr (C++ member)

json_autoptr::release (C++ function) json_autoptr::~json_autoptr (C++ function) json_boolean (C macro) json_dump_std_string (C++ function) JSONStreamHelper (C++ class) JSONStreamHelper::_fp (C++ member) JSONStreamHelper::get_read_fn (C++ function) JSONStreamHelper::JSONStreamHelper (C++ function) JSONStreamHelper::write (C++ function) JSONStreamHelper::~JSONStreamHelper (C++ function)

M

main (C++ function) main_align (C++ function) main_call (C++ function) main_circularize (C++ function) main_compare (C++ function) main_concat (C++ function) main_construct (C++ function) main_deconstruct (C++ function) main_filter (C++ function) main_find (C++ function) main_genotype (C++ function) main_ids (C++ function) main_index (C++ function) main_join (C++ function) main_kmers (C++ function) main_locify (C++ function)

main_map (C++ function) main_mod (C++ function) main_msga (C++ function) main_paths (C++ function) main_pileup (C++ function) main_scrub (C++ function) main_sim (C++ function) main_simplify (C++ function) main_stats (C++ function) main_surject (C++ function) main_test (C++ function) main_translate (C++ function) main_validate (C++ function) main_vectorize (C++ function) main_version (C++ function) main_view (C++ function)

O

operator< (C++ function)

operator== (C++ function) OVERLOAD_PAIR_HASH (C macro)

P

pb2json (C++ function), [1]

Q

QualAdjAligner::align (C++ function) QualAdjAligner::align_global_banded (C++ function) QualAdjAligner::align_global_banded_multi (C++ function) QualAdjAligner::init_mapping_quality (C++ function)

QualAdjAligner::init_quality_adjusted_scores (C++ function) QualAdjAligner::QualAdjAligner (C++ function) QualAdjAligner::score_exact_match (C++ function) QualAdjAligner::~QualAdjAligner (C++ function) quality_scale_factor (C++ member)

S

sdsl (C++ type) stCactusGraph (C++ type) stCactusNode (C++ type) std (C++ type) std::hash::operator() (C++ function), [1] std::hash<pair<A, B>> (C++ class) std::hash<vg::NodeSide> (C++ class)

stream (C++ type) stream::for_each (C++ function), [1] stream::for_each_parallel (C++ function), [1] stream::write (C++ function) stream::write_buffered (C++ function) supbub (C++ type) swap_remove (C++ function)

U

USE_DENSE_HASH (C macro)

V

vcfh (C++ type) Vectorizer (C++ class) Vectorizer::add_bv (C++ function) Vectorizer::add_name (C++ function) Vectorizer::alignment_to_a_hot (C++ function) Vectorizer::alignment_to_custom_score (C++ function) Vectorizer::alignment_to_identity_hot (C++ function) Vectorizer::alignment_to_onehot (C++ function) Vectorizer::emit (C++ function) Vectorizer::format (C++ function) Vectorizer::my_names (C++ member) Vectorizer::my_vectors (C++ member) Vectorizer::my_xg (C++ member) Vectorizer::output_names (C++ member) Vectorizer::output_tabbed (C++ member) Vectorizer::output_wabbit_map (C++ function) Vectorizer::Vectorizer (C++ function) Vectorizer::wabbit_map (C++ member) Vectorizer::wabbitize (C++ function) Vectorizer::~Vectorizer (C++ function) vg (C++ type) vg::add_alt_allele (C++ function) vg::adjacent_mappings (C++ function) vg::Aligner (C++ class) vg::Aligner::gap_extension (C++ member) vg::Aligner::gap_open (C++ member) vg::Aligner::log_base (C++ member) vg::Aligner::match (C++ member) vg::Aligner::mismatch (C++ member) vg::Aligner::nt_table (C++ member) vg::Aligner::score_matrix (C++ member) vg::Aligner::topological_sort (C++ function) vg::Aligner::visit_node (C++ function) vg::Alignment (C++ class) vg::Alignment::fragment (C++ member) vg::Alignment::fragment_next (C++ member) vg::Alignment::fragment_prev (C++ member) vg::Alignment::identity (C++ member) vg::Alignment::is_secondary (C++ member) vg::Alignment::locus (C++ member) vg::Alignment::mapping_quality (C++ member) vg::Alignment::name (C++ member) vg::Alignment::path (C++ member) vg::Alignment::quality (C++ member) vg::Alignment::query_position (C++ member) vg::Alignment::read_group (C++ member) vg::Alignment::sample_name (C++ member) vg::Alignment::score (C++ member) vg::Alignment::sequence (C++ member) vg::alignment_ends (C++ function) vg::alignment_from_length (C++ function) vg::alignment_quality_char_to_short (C++ function) vg::alignment_quality_per_node (C++ function) vg::alignment_quality_short_to_char (C++ function) vg::alignment_to_bam (C++ function) vg::alignment_to_length (C++ function) vg::alignment_to_sam (C++ function) vg::allATGC (C++ function) vg::allele_to_string (C++ function) vg::append_path (C++ function) vg::Approx (C++ class) vg::avgSup (C++ function) vg::balanced_kmers (C++ function) vg::balanced_stride (C++ function) vg::BAM_DNA_LOOKUP (C++ member) vg::bam_to_alignment (C++ function) vg::BandedGlobalAligner (C++ class) vg::BandedGlobalAligner::adjust_for_base_quality (C++ member) vg::BandedGlobalAligner::alignment (C++ member) vg::BandedGlobalAligner::alt_alignments (C++ member) vg::BandedGlobalAligner::AltTracebackStack (C++ class) vg::BandedGlobalAligner::AltTracebackStack::Deflection (C++ class) vg::BandedGlobalAligner::BABuilder (C++ class) vg::BandedGlobalAligner::BAMatrix (C++ class) vg::BandedGlobalAligner::banded_matrices (C++ member) vg::BandedGlobalAligner::InsertCol (C++ class) vg::BandedGlobalAligner::InsertRow (C++ class) vg::BandedGlobalAligner::Match (C++ class) vg::BandedGlobalAligner::matrix_t (C++ type) vg::BandedGlobalAligner::max_multi_alns (C++ member) vg::BandedGlobalAligner::node_id_to_idx (C++ member) vg::BandedGlobalAligner::sink_nodes (C++ member) vg::BandedGlobalAligner::source_nodes (C++ member) vg::BandedGlobalAligner::topological_order (C++ member) vg::BandedGlobalAligner<IntType>::AltTracebackStack::alt_tracebacks (C++ member) vg::BandedGlobalAligner<IntType>::AltTracebackStack::curr_deflxn (C++ member) vg::BandedGlobalAligner<IntType>::AltTracebackStack::curr_traceback (C++ member) vg::BandedGlobalAligner<IntType>::AltTracebackStack::Deflection::col_idx (C++ member) vg::BandedGlobalAligner<IntType>::AltTracebackStack::Deflection::from_node_id (C++ member) vg::BandedGlobalAligner<IntType>::AltTracebackStack::Deflection::row_idx (C++ member) vg::BandedGlobalAligner<IntType>::AltTracebackStack::Deflection::to_matrix (C++ member) vg::BandedGlobalAligner<IntType>::AltTracebackStack::Deflection::to_node_id (C++ member) vg::BandedGlobalAligner<IntType>::AltTracebackStack::max_multi_alns (C++ member) vg::BandedGlobalAligner<IntType>::BABuilder::alignment (C++ member) vg::BandedGlobalAligner<IntType>::BABuilder::current_node (C++ member) vg::BandedGlobalAligner<IntType>::BABuilder::edit_length (C++ member) vg::BandedGlobalAligner<IntType>::BABuilder::edit_read_end_idx (C++ member) vg::BandedGlobalAligner<IntType>::BABuilder::mapping_edits (C++ member) vg::BandedGlobalAligner<IntType>::BABuilder::matching (C++ member) vg::BandedGlobalAligner<IntType>::BABuilder::matrix_state (C++ member) vg::BandedGlobalAligner<IntType>::BABuilder::node_mappings (C++ member) vg::BandedGlobalAligner<IntType>::BAMatrix::alignment (C++ member) vg::BandedGlobalAligner<IntType>::BAMatrix::bottom_diag (C++ member) vg::BandedGlobalAligner<IntType>::BAMatrix::cumulative_seq_len (C++ member) vg::BandedGlobalAligner<IntType>::BAMatrix::insert_col (C++ member) vg::BandedGlobalAligner<IntType>::BAMatrix::insert_row (C++ member) vg::BandedGlobalAligner<IntType>::BAMatrix::match (C++ member) vg::BandedGlobalAligner<IntType>::BAMatrix::node (C++ member) vg::BandedGlobalAligner<IntType>::BAMatrix::num_seeds (C++ member) vg::BandedGlobalAligner<IntType>::BAMatrix::seeds (C++ member) vg::BandedGlobalAligner<IntType>::BAMatrix::top_diag (C++ member) vg::BasePileup (C++ class) vg::BasePileup::bases (C++ member) vg::BasePileup::num_bases (C++ member) vg::BasePileup::qualities (C++ member) vg::BasePileup::ref_base (C++ member) vg::binomial_cmf_ln (C++ function) vg::Bubble (C++ class) vg::Bubble::acyclic (C++ member) vg::Bubble::chain_offsets (C++ member) vg::Bubble::contents (C++ member) vg::Bubble::end (C++ member) vg::Bubble::start (C++ member) vg::BubbleTree (C++ type) vg::cactus_to_vg (C++ function) vg::cactusify (C++ function) vg::CactusSide (C++ class) vg::CactusSide::is_end (C++ member) vg::CactusSide::node (C++ member) vg::CactusSiteFinder (C++ class) vg::CactusSiteFinder::CactusSiteFinder (C++ function) vg::CactusSiteFinder::for_each_site_parallel (C++ function) vg::CactusSiteFinder::graph (C++ member) vg::CactusSiteFinder::hint_path_name (C++ member) vg::CactusSiteFinder::~CactusSiteFinder (C++ function) vg::Caller (C++ class) vg::Caller::_augmented_edges (C++ member) vg::Caller::_bridge_alts (C++ member) vg::Caller::_buffer_size (C++ member) vg::Caller::_call_graph (C++ member) vg::Caller::_called_edges (C++ member) vg::Caller::_default_quality (C++ member) vg::Caller::_deletion_supports (C++ member) vg::Caller::_graph (C++ member) vg::Caller::_het_log_prior (C++ member) vg::Caller::_hom_log_prior (C++ member) vg::Caller::_insert_calls (C++ member) vg::Caller::_insert_supports (C++ member) vg::Caller::_inserted_nodes (C++ member) vg::Caller::_insertion_supports (C++ member) vg::Caller::_leave_uncalled (C++ member) vg::Caller::_max_depth (C++ member) vg::Caller::_max_id (C++ member) vg::Caller::_max_strand_bias (C++ member) vg::Caller::_min_depth (C++ member) vg::Caller::_min_frac (C++ member) vg::Caller::_min_log_likelihood (C++ member) vg::Caller::_min_support (C++ member) vg::Caller::_node (C++ member) vg::Caller::_node_calls (C++ member) vg::Caller::_node_divider (C++ member) vg::Caller::_node_supports (C++ member) vg::Caller::_text_calls (C++ member) vg::Caller::_visited_nodes (C++ member) vg::Caller::base_log_likelihood (C++ function) vg::Caller::call_base_pileup (C++ function) vg::Caller::call_cat (C++ function) vg::Caller::call_edge_pileup (C++ function) vg::Caller::call_node_pileup (C++ function) vg::Caller::Caller (C++ function) vg::Caller::clear (C++ function) vg::Caller::compute_top_frequencies (C++ function) vg::Caller::create_augmented_edge (C++ function) vg::Caller::create_node_calls (C++ function) vg::Caller::Default_default_quality (C++ member) vg::Caller::Default_het_prior (C++ member) vg::Caller::Default_max_depth (C++ member) vg::Caller::Default_max_strand_bias (C++ member) vg::Caller::Default_min_depth (C++ member) vg::Caller::Default_min_frac (C++ member) vg::Caller::Default_min_log_likelihood (C++ member) vg::Caller::Default_min_support (C++ member) vg::Caller::EdgeHash (C++ type) vg::Caller::EdgeSupHash (C++ type) vg::Caller::Genotype (C++ type) vg::Caller::InsertionHash (C++ type) vg::Caller::InsertionRecord (C++ class) vg::Caller::InsertionRecord::node (C++ member) vg::Caller::InsertionRecord::orig_id (C++ member) vg::Caller::InsertionRecord::orig_offset (C++ member) vg::Caller::InsertionRecord::sup (C++ member) vg::Caller::Log_zero (C++ member) vg::Caller::map_paths (C++ function) vg::Caller::missing_call (C++ function) vg::Caller::NodeOffSide (C++ type) vg::Caller::ref_call (C++ function) vg::Caller::safe_log (C++ function) vg::Caller::update_call_graph (C++ function) vg::Caller::verify_path (C++ function) vg::Caller::write_call_graph (C++ function) vg::Caller::write_edge_tsv (C++ function) vg::Caller::write_nd_tsv (C++ function) vg::Caller::write_node_tsv (C++ function) vg::Caller::~Caller (C++ function) vg::choose_ln (C++ function) vg::cigar_against_path (C++ function) vg::cigar_string (C++ function) vg::Colors (C++ class) vg::Colors::Colors (C++ function), [1] vg::Colors::colors (C++ member) vg::Colors::hashed (C++ function) vg::Colors::random (C++ function) vg::Colors::rng (C++ member) vg::Colors::~Colors (C++ function) vg::complement (C++ member) vg::compute_side_components (C++ function) vg::concat_mappings (C++ function) vg::concat_paths (C++ function) vg::ConsistencyCalculator (C++ class) vg::ConsistencyCalculator::calculate_consistency (C++ function) vg::ConsistencyCalculator::~ConsistencyCalculator (C++ function) vg::ConstructedChunk (C++ class) vg::ConstructedChunk::graph (C++ member) vg::ConstructedChunk::left_ends (C++ member) vg::ConstructedChunk::max_id (C++ member) vg::ConstructedChunk::right_ends (C++ member) vg::Constructor (C++ class) vg::Constructor::add_name_mapping (C++ function) vg::Constructor::allowed_vcf_names (C++ member) vg::Constructor::allowed_vcf_regions (C++ member) vg::Constructor::alt_paths (C++ member) vg::Constructor::bases_per_chunk (C++ member) vg::Constructor::chain_deletions (C++ member) vg::Constructor::construct_chunk (C++ function) vg::Constructor::construct_graph (C++ function), [1] vg::Constructor::fasta_to_vcf (C++ function) vg::Constructor::fasta_to_vcf_renames (C++ member) vg::Constructor::flat (C++ member) vg::Constructor::greedy_pieces (C++ member) vg::Constructor::max_node_size (C++ member) vg::Constructor::vars_per_chunk (C++ member) vg::Constructor::vcf_to_fasta (C++ function) vg::Constructor::vcf_to_fasta_renames (C++ member) vg::create_ref_allele (C++ function) vg::cut_edit_at_from (C++ function) vg::cut_edit_at_to (C++ function) vg::cut_mapping (C++ function), [1] vg::cut_path (C++ function), [1] vg::decompose (C++ function) vg::Deconstructor (C++ class) vg::Deconstructor::compact (C++ function) vg::Deconstructor::contains_nested (C++ function) vg::Deconstructor::dagify_my_vg (C++ function) vg::Deconstructor::Deconstructor (C++ function), [1] vg::Deconstructor::get_all_superbubbles (C++ function) vg::Deconstructor::id_to_bub (C++ member) vg::Deconstructor::init (C++ function) vg::Deconstructor::is_nested (C++ function) vg::Deconstructor::mask_file (C++ member) vg::Deconstructor::my_dagify_translation (C++ member) vg::Deconstructor::my_max_component_length (C++ member) vg::Deconstructor::my_max_length (C++ member) vg::Deconstructor::my_sbs (C++ member) vg::Deconstructor::my_superbubbles (C++ member) vg::Deconstructor::my_translation (C++ member) vg::Deconstructor::my_unroll_translation (C++ member) vg::Deconstructor::my_vg (C++ member) vg::Deconstructor::my_xg (C++ member) vg::Deconstructor::nt_to_ids (C++ function) vg::Deconstructor::report_superbubble (C++ function) vg::Deconstructor::reverse_topo_order (C++ member) vg::Deconstructor::sb2vcf (C++ function) vg::Deconstructor::set_xg (C++ function) vg::Deconstructor::translate_id (C++ function) vg::Deconstructor::unroll_my_vg (C++ function) vg::Deconstructor::~Deconstructor (C++ function) vg::default_gap_extension (C++ member) vg::default_gap_open (C++ member) vg::default_gc_content (C++ member) vg::default_match (C++ member) vg::default_max_qual_score (C++ member) vg::default_max_scaled_score (C++ member) vg::default_mismatch (C++ member) vg::divergence (C++ function) vg::Edge (C++ class) vg::Edge::from (C++ member) vg::Edge::from_start (C++ member) vg::Edge::overlap (C++ member) vg::Edge::to (C++ member) vg::Edge::to_end (C++ member) vg::EdgePileup (C++ class) vg::EdgePileup::edge (C++ member) vg::EdgePileup::num_forward_reads (C++ member) vg::EdgePileup::num_reads (C++ member) vg::EdgePileup::qualities (C++ member) vg::Edit (C++ class) vg::Edit::from_length (C++ member) vg::Edit::sequence (C++ member) vg::Edit::to_length (C++ member) vg::edit_is_deletion (C++ function) vg::edit_is_insertion (C++ function) vg::edit_is_match (C++ function) vg::edit_is_sub (C++ function) vg::entropy (C++ function) vg::Exact (C++ class) vg::extend_alignment (C++ function) vg::extend_path (C++ function) vg::factorial_ln (C++ function) vg::fastq_for_each (C++ function) vg::fastq_paired_interleaved_for_each (C++ function) vg::fastq_paired_interleaved_for_each_parallel (C++ function) vg::fastq_paired_two_files_for_each (C++ function) vg::fastq_paired_two_files_for_each_parallel (C++ function) vg::fastq_unpaired_for_each (C++ function) vg::fastq_unpaired_for_each_parallel (C++ function) vg::fill_ultrabubble_contents (C++ function) vg::Filter (C++ class) vg::Filter::avg_qual_filter (C++ function) vg::Filter::coverage_filter (C++ function) vg::Filter::depth_filter (C++ function) vg::Filter::do_path_divergence (C++ member) vg::Filter::do_reversing (C++ member) vg::Filter::Filter (C++ function) vg::Filter::filter_matches (C++ member) vg::Filter::get_do_path_divergence (C++ function) vg::Filter::get_do_reversing (C++ function) vg::Filter::get_filter_matches (C++ function) vg::Filter::get_inverse (C++ function) vg::Filter::get_min_avg_qual (C++ function) vg::Filter::get_min_depth (C++ function) vg::Filter::get_min_percent_identity (C++ function) vg::Filter::get_min_qual (C++ function) vg::Filter::get_remove_failing_edits (C++ function) vg::Filter::get_soft_clip_limit (C++ function) vg::Filter::get_split_read_limit (C++ function) vg::Filter::get_window_length (C++ function) vg::Filter::inverse (C++ member) vg::Filter::kmer_filter (C++ function) vg::Filter::min_avg_qual (C++ member) vg::Filter::min_cov (C++ member) vg::Filter::min_depth (C++ member) vg::Filter::min_percent_identity (C++ member) vg::Filter::min_qual (C++ member) vg::Filter::my_vg (C++ member) vg::Filter::my_xg_idx (C++ member) vg::Filter::path_divergence_filter (C++ function) vg::Filter::percent_identity_filter (C++ function) vg::Filter::pos_to_edit_to_depth (C++ member) vg::Filter::pos_to_qual (C++ member) vg::Filter::qual_filter (C++ function) vg::Filter::qual_offset (C++ member) vg::Filter::remove_failing_edits (C++ member) vg::Filter::reversing_filter (C++ function) vg::Filter::set_avg_qual (C++ function) vg::Filter::set_filter_matches (C++ function) vg::Filter::set_inverse (C++ function) vg::Filter::set_min_depth (C++ function) vg::Filter::set_min_percent_identity (C++ function) vg::Filter::set_min_qual (C++ function) vg::Filter::set_my_vg (C++ function) vg::Filter::set_my_xg_idx (C++ function) vg::Filter::set_path_divergence (C++ function) vg::Filter::set_remove_failing_edits (C++ function) vg::Filter::set_reversing (C++ function) vg::Filter::set_soft_clip_limit (C++ function) vg::Filter::set_split_read_limit (C++ function) vg::Filter::set_window_length (C++ function) vg::Filter::soft_clip_filter (C++ function) vg::Filter::soft_clip_limit (C++ member) vg::Filter::split_read_filter (C++ function) vg::Filter::split_read_limit (C++ member) vg::Filter::window_length (C++ member) vg::Filter::~Filter (C++ function) vg::first_path_position (C++ function) vg::FixedGenotypePriorCalculator (C++ class) vg::FixedGenotypePriorCalculator::calculate_log_prior (C++ function) vg::FixedGenotypePriorCalculator::heterozygous_prior_ln (C++ member) vg::FixedGenotypePriorCalculator::homozygous_prior_ln (C++ member) vg::FixedGenotypePriorCalculator::~FixedGenotypePriorCalculator (C++ function) vg::flip_nodes (C++ function) vg::from_length (C++ function) vg::from_length_after_pos (C++ function) vg::from_length_before_pos (C++ function) vg::gam_paired_interleaved_for_each_parallel (C++ function) vg::gamma_ln (C++ function) vg::gcsa_nodes_to_positions (C++ function) vg::Genotype (C++ class) vg::Genotype::allele (C++ member) vg::Genotype::is_phased (C++ member) vg::Genotype::likelihood (C++ member) vg::Genotype::log_likelihood (C++ member) vg::Genotype::log_posterior (C++ member) vg::Genotype::log_prior (C++ member) vg::GenotypeLikelihoodCalculator (C++ class) vg::GenotypeLikelihoodCalculator::calculate_log_likelihood (C++ function) vg::GenotypeLikelihoodCalculator::~GenotypeLikelihoodCalculator (C++ function) vg::GenotypePriorCalculator (C++ class) vg::GenotypePriorCalculator::calculate_log_prior (C++ function) vg::GenotypePriorCalculator::~GenotypePriorCalculator (C++ function) vg::Genotyper (C++ class) vg::Genotyper::Affinity (C++ class) vg::Genotyper::Affinity::Affinity (C++ function), [1] vg::Genotyper::Affinity::affinity (C++ member) vg::Genotyper::Affinity::consistent (C++ member) vg::Genotyper::Affinity::is_reverse (C++ member) vg::Genotyper::Affinity::likelihood_ln (C++ member) vg::Genotyper::Affinity::score (C++ member) vg::Genotyper::alignment_qual_score (C++ function) vg::Genotyper::all_sites (C++ member) vg::Genotyper::allele_ambiguity_log_probs (C++ function) vg::Genotyper::dagify_steps (C++ member) vg::Genotyper::default_sequence_quality (C++ member) vg::Genotyper::edge_allele_labels (C++ function) vg::Genotyper::find_sites_with_cactus (C++ function) vg::Genotyper::find_sites_with_supbub (C++ function) vg::Genotyper::genotype_site (C++ function) vg::Genotyper::get_affinities (C++ function) vg::Genotyper::get_affinities_fast (C++ function) vg::Genotyper::get_genotype_log_likelihood (C++ function) vg::Genotyper::get_genotype_log_prior (C++ function) vg::Genotyper::get_paths_through_site (C++ function) vg::Genotyper::get_qualities_in_site (C++ function) vg::Genotyper::get_site_reference_bounds (C++ function) vg::Genotyper::get_traversal_of_site (C++ function) vg::Genotyper::hash_ambiguous_allele_set (C++ class) vg::Genotyper::hash_ambiguous_allele_set::operator() (C++ function) vg::Genotyper::hash_node_traversal (C++ class) vg::Genotyper::hash_node_traversal::operator() (C++ function) vg::Genotyper::hash_oriented_edge (C++ class) vg::Genotyper::hash_oriented_edge::operator() (C++ function) vg::Genotyper::het_prior_logprob (C++ member) vg::Genotyper::locus_to_variant (C++ function) vg::Genotyper::max_het_bias (C++ member) vg::Genotyper::max_path_search_steps (C++ member) vg::Genotyper::min_consistent_per_strand (C++ member) vg::Genotyper::min_recurrence (C++ member) vg::Genotyper::min_score_per_base (C++ member) vg::Genotyper::normal_aligner (C++ member) vg::Genotyper::print_statistics (C++ function) vg::Genotyper::quality_aligner (C++ member) vg::Genotyper::realign_indels (C++ member) vg::Genotyper::report_site (C++ function) vg::Genotyper::report_site_traversal (C++ function) vg::Genotyper::run (C++ function) vg::Genotyper::Site (C++ class) vg::Genotyper::Site::contents (C++ member) vg::Genotyper::Site::end (C++ member) vg::Genotyper::Site::start (C++ member) vg::Genotyper::site_reference_length_histogram (C++ member) vg::Genotyper::site_traversals (C++ member) vg::Genotyper::start_vcf (C++ function) vg::Genotyper::translator (C++ member) vg::Genotyper::traversals_to_string (C++ function) vg::Genotyper::unfold_max_length (C++ member) vg::Genotyper::use_mapq (C++ member) vg::Genotyper::write_vcf_header (C++ function) vg::get_id (C++ function) vg::get_input_file (C++ function), [1] vg::get_input_file_name (C++ function) vg::get_is_rev (C++ function) vg::get_next_alignment_from_fastq (C++ function) vg::get_next_alignment_pair_from_fastqs (C++ function) vg::get_next_interleaved_alignment_pair_from_fastq (C++ function) vg::get_offset (C++ function) vg::get_or_make_variant_id (C++ function) vg::get_superbubbles (C++ function), [1] vg::get_thread_count (C++ function) vg::Graph (C++ class) vg::Graph::edge (C++ member) vg::Graph::node (C++ member) vg::Graph::path (C++ member) vg::hash_alignment (C++ function) vg::hash_map (C++ class) vg::hash_map::hash_map (C++ function), [1] vg::hash_map<K *, V> (C++ class) vg::hts_file_header (C++ function) vg::hts_for_each (C++ function) vg::hts_for_each_parallel (C++ function) vg::hts_string_header (C++ function) vg::id (C++ function) vg::id_t (C++ type) vg::identity (C++ function) vg::increment_node_mapping_ids (C++ function) vg::Index (C++ class) vg::Index::alignment_entry_to_string (C++ function) vg::Index::approx_size_of_kmer_matches (C++ function) vg::Index::approx_sizes_of_kmer_matches (C++ function) vg::Index::base_entry_to_string (C++ function) vg::Index::batch_edge (C++ function) vg::Index::batch_kmer (C++ function) vg::Index::batch_node (C++ function) vg::Index::block_cache_size (C++ member) vg::Index::bulk_load (C++ member) vg::Index::close (C++ function) vg::Index::column_family_options (C++ member) vg::Index::compact (C++ function) vg::Index::compare_kmers (C++ function) vg::Index::cross_alignment (C++ function) vg::Index::db (C++ member) vg::Index::db_options (C++ member) vg::Index::dump (C++ function) vg::Index::end_sep (C++ member) vg::Index::entry_to_string (C++ function) vg::Index::expand_context (C++ function) vg::Index::first_kmer_key (C++ function) vg::Index::flush (C++ function) vg::Index::for_alignment_in_range (C++ function) vg::Index::for_alignment_to_node (C++ function) vg::Index::for_alignment_to_nodes (C++ function) vg::Index::for_all (C++ function) vg::Index::for_base_alignments (C++ function) vg::Index::for_each_alignment (C++ function) vg::Index::for_each_mapping (C++ function) vg::Index::for_graph_range (C++ function) vg::Index::for_kmer_range (C++ function) vg::Index::for_range (C++ function) vg::Index::get_alignments (C++ function), [1] vg::Index::get_connected_nodes (C++ function) vg::Index::get_context (C++ function) vg::Index::get_edge (C++ function) vg::Index::get_edges_on_end (C++ function) vg::Index::get_edges_on_start (C++ function) vg::Index::get_kmer_positions (C++ function), [1] vg::Index::get_kmer_subgraph (C++ function) vg::Index::get_mappings (C++ function) vg::Index::get_max_path_id (C++ function) vg::Index::get_metadata (C++ function) vg::Index::get_nearest_node_next_path_member (C++ function) vg::Index::get_nearest_node_prev_path_member (C++ function) vg::Index::get_node (C++ function) vg::Index::get_node_path (C++ function) vg::Index::get_node_path_relative_position (C++ function) vg::Index::get_nodes_next (C++ function) vg::Index::get_nodes_prev (C++ function) vg::Index::get_path (C++ function) vg::Index::get_path_id (C++ function) vg::Index::get_path_name (C++ function) vg::Index::get_range (C++ function) vg::Index::GetOptions (C++ function) vg::Index::graph_entry_to_string (C++ function) vg::Index::graph_key_type (C++ function) vg::Index::Index (C++ function), [1] vg::Index::is_open (C++ member) vg::Index::key_for_alignment (C++ function) vg::Index::key_for_alignment_prefix (C++ function) vg::Index::key_for_base (C++ function) vg::Index::key_for_edge_on_end (C++ function) vg::Index::key_for_edge_on_start (C++ function) vg::Index::key_for_kmer (C++ function) vg::Index::key_for_mapping (C++ function) vg::Index::key_for_mapping_prefix (C++ function) vg::Index::key_for_metadata (C++ function) vg::Index::key_for_node (C++ function) vg::Index::key_for_node_path_position (C++ function) vg::Index::key_for_path_position (C++ function) vg::Index::key_for_traversal (C++ function) vg::Index::key_prefix_for_edges_on_node_end (C++ function) vg::Index::key_prefix_for_edges_on_node_start (C++ function) vg::Index::key_prefix_for_kmer (C++ function) vg::Index::key_prefix_for_node_path (C++ function) vg::Index::key_prefix_for_traversal (C++ function) vg::Index::kmer_entry_to_string (C++ function) vg::Index::kmer_matches (C++ function) vg::Index::load_graph (C++ function) vg::Index::load_paths (C++ function) vg::Index::mapping_entry_to_string (C++ function) vg::Index::mem_env (C++ member) vg::Index::metadata_entry_to_string (C++ function) vg::Index::name (C++ member) vg::Index::new_path_id (C++ function) vg::Index::node_path_position (C++ function) vg::Index::node_path_to_string (C++ function) vg::Index::open (C++ function) vg::Index::open_for_bulk_load (C++ function) vg::Index::open_for_write (C++ function) vg::Index::open_read_only (C++ function) vg::Index::parse_alignment (C++ function) vg::Index::parse_base (C++ function) vg::Index::parse_edge (C++ function), [1] vg::Index::parse_kmer (C++ function) vg::Index::parse_mapping (C++ function) vg::Index::parse_node (C++ function) vg::Index::parse_node_path (C++ function) vg::Index::parse_path_position (C++ function) vg::Index::parse_traversal (C++ function) vg::Index::path_first_node (C++ function) vg::Index::path_id_prefix (C++ function) vg::Index::path_last_node (C++ function) vg::Index::path_layout (C++ function) vg::Index::path_name_prefix (C++ function) vg::Index::path_position_to_string (C++ function) vg::Index::path_relative_mapping (C++ function) vg::Index::paths_by_id (C++ function) vg::Index::position_entry_to_string (C++ function) vg::Index::prune_kmers (C++ function) vg::Index::put_alignment (C++ function) vg::Index::put_base (C++ function) vg::Index::put_edge (C++ function) vg::Index::put_kmer (C++ function) vg::Index::put_mapping (C++ function) vg::Index::put_max_path_id (C++ function) vg::Index::put_metadata (C++ function) vg::Index::put_node (C++ function) vg::Index::put_node_path (C++ function) vg::Index::put_path_id_to_name (C++ function) vg::Index::put_path_name_to_id (C++ function) vg::Index::put_path_position (C++ function) vg::Index::put_traversal (C++ function) vg::Index::remember_kmer_size (C++ function) vg::Index::reset_options (C++ function) vg::Index::rng (C++ member) vg::Index::start_sep (C++ member) vg::Index::store_batch (C++ function) vg::Index::store_path (C++ function) vg::Index::store_paths (C++ function) vg::Index::stored_kmer_sizes (C++ function) vg::Index::surject_alignment (C++ function) vg::Index::threads (C++ member) vg::Index::traversal_entry_to_string (C++ function) vg::Index::use_snappy (C++ member) vg::Index::write_options (C++ member) vg::Index::~Index (C++ function) vg::index_positions (C++ function) vg::indexOpenException (C++ class) vg::indexOpenException::indexOpenException (C++ function) vg::indexOpenException::message (C++ member) vg::indexOpenException::what (C++ function) vg::is_empty (C++ function) vg::is_match (C++ function) vg::is_number (C++ function), [1] vg::is_rev (C++ function) vg::keyNotFoundException (C++ class) vg::keyNotFoundException::what (C++ function) vg::KmerMatch (C++ class) vg::KmerMatch::backward (C++ member) vg::KmerMatch::node_id (C++ member) vg::KmerMatch::position (C++ member) vg::KmerMatch::sequence (C++ member) vg::KmerPosition (C++ class) vg::KmerPosition::kmer (C++ member) vg::KmerPosition::next_chars (C++ member) vg::KmerPosition::next_positions (C++ member) vg::KmerPosition::pos (C++ member) vg::KmerPosition::prev_chars (C++ member) vg::last_path_position (C++ function) vg::Locus (C++ class) vg::Locus::allele (C++ member) vg::Locus::genotype (C++ member) vg::Locus::name (C++ member) vg::Locus::overall_support (C++ member) vg::Locus::support (C++ member) vg::logprob_add (C++ function) vg::logprob_invert (C++ function) vg::logprob_sum (C++ function) vg::logprob_to_phred (C++ function) vg::logprob_to_prob (C++ function) vg::make_pos_t (C++ function), [1] vg::make_position (C++ function), [1] vg::make_variant_id (C++ function) vg::map_keys_to_set (C++ function) vg::Mapper (C++ class) vg::Mapper::accept_identity (C++ member) vg::Mapper::adjacent_positions (C++ function) vg::Mapper::adjust_alignments_for_base_quality (C++ member) vg::Mapper::align (C++ function), [1] vg::Mapper::align_banded (C++ function) vg::Mapper::align_mate_in_window (C++ function) vg::Mapper::align_mem_multi (C++ function) vg::Mapper::align_multi (C++ function) vg::Mapper::align_multi_internal (C++ function) vg::Mapper::align_multi_kmers (C++ function) vg::Mapper::align_paired (C++ function) vg::Mapper::align_paired_multi (C++ function) vg::Mapper::align_threaded (C++ function) vg::Mapper::align_to_graph (C++ function) vg::Mapper::alignment_mean_path_positions (C++ function) vg::Mapper::alignment_subgraph (C++ function) vg::Mapper::alignment_threads (C++ member) vg::Mapper::alignments_consistent (C++ function) vg::Mapper::always_rescue (C++ member) vg::Mapper::approx_pair_fragment_length (C++ function) vg::Mapper::best_clusters (C++ member) vg::Mapper::cached_fragment_length_mean (C++ member) vg::Mapper::cached_fragment_length_stdev (C++ member) vg::Mapper::check_alignment (C++ function) vg::Mapper::check_mems (C++ function) vg::Mapper::clear_aligners (C++ function) vg::Mapper::cluster_min (C++ member) vg::Mapper::compute_mapping_qualities (C++ function), [1] vg::Mapper::context_depth (C++ member) vg::Mapper::debug (C++ member) vg::Mapper::estimate_gc_content (C++ function) vg::Mapper::extra_pairing_multimaps (C++ member) vg::Mapper::filter_and_process_multimaps (C++ function) vg::Mapper::find_forward_mems (C++ function) vg::Mapper::find_smems (C++ function) vg::Mapper::fragment_length_cache_size (C++ member) vg::Mapper::fragment_length_estimate_interval (C++ member) vg::Mapper::fragment_length_mean (C++ function) vg::Mapper::fragment_length_stdev (C++ function) vg::Mapper::fragment_lengths (C++ member) vg::Mapper::fragment_max (C++ member) vg::Mapper::fragment_sigma (C++ member) vg::Mapper::fragment_size (C++ member) vg::Mapper::gcsa (C++ member) vg::Mapper::get_mem_hits_if_under_max (C++ function) vg::Mapper::get_node_cache (C++ function) vg::Mapper::get_node_length (C++ function) vg::Mapper::get_qual_adj_aligner (C++ function) vg::Mapper::get_regular_aligner (C++ function) vg::Mapper::greedy_accept (C++ member) vg::Mapper::hit_max (C++ member) vg::Mapper::hit_size_threshold (C++ member) vg::Mapper::imperfect_pairs_to_retry (C++ member) vg::Mapper::index (C++ member) vg::Mapper::init_aligner (C++ function) vg::Mapper::init_node_cache (C++ function) vg::Mapper::kmer_min (C++ member) vg::Mapper::kmer_sensitivity_step (C++ member) vg::Mapper::kmer_sizes (C++ member) vg::Mapper::lcp (C++ member) vg::Mapper::Mapper (C++ function), [1], [2], [3] vg::Mapper::mapping_quality_method (C++ member) vg::Mapper::max_attempts (C++ member) vg::Mapper::max_multimaps (C++ member) vg::Mapper::max_query_graph_ratio (C++ member) vg::Mapper::max_softclip_iterations (C++ member) vg::Mapper::max_target_factor (C++ member) vg::Mapper::max_thread_gap (C++ member) vg::Mapper::mem_threading (C++ member) vg::Mapper::mem_to_alignment (C++ function) vg::Mapper::mem_to_alignments (C++ function) vg::Mapper::mems_id_clusters_to_alignments (C++ function) vg::Mapper::mems_pos_clusters_to_alignments (C++ function) vg::Mapper::mems_to_alignment (C++ function) vg::Mapper::min_identity (C++ member) vg::Mapper::min_kmer_entropy (C++ member) vg::Mapper::min_mem_length (C++ member) vg::Mapper::next_pos_chars (C++ function) vg::Mapper::node_cache (C++ member) vg::Mapper::patch_alignment (C++ function) vg::Mapper::pos_char (C++ function) vg::Mapper::prefer_forward (C++ member) vg::Mapper::qual_adj_aligners (C++ member) vg::Mapper::record_fragment_length (C++ function) vg::Mapper::regular_aligners (C++ member) vg::Mapper::resolve_banded_multi (C++ function) vg::Mapper::resolve_paired_mems (C++ function) vg::Mapper::resolve_softclips (C++ function) vg::Mapper::score_sort_and_deduplicate_alignments (C++ function) vg::Mapper::sequence_positions (C++ function) vg::Mapper::set_alignment_scores (C++ function) vg::Mapper::since_last_fragment_length_estimate (C++ member) vg::Mapper::softclip_threshold (C++ member) vg::Mapper::surject_alignment (C++ function) vg::Mapper::thread_extension (C++ member) vg::Mapper::walk_match (C++ function), [1] vg::Mapper::xindex (C++ member) vg::Mapper::~Mapper (C++ function) vg::Mapping (C++ class) vg::Mapping::edit (C++ member) vg::Mapping::position (C++ member) vg::Mapping::rank (C++ member) vg::mapping_cigar (C++ function) vg::mapping_ends_in_deletion (C++ function) vg::mapping_from_length (C++ function) vg::mapping_is_match (C++ function) vg::mapping_is_simple_match (C++ function) vg::mapping_is_total_deletion (C++ function) vg::mapping_sequence (C++ function), [1]

vg::mapping_starts_in_deletion (C++ function) vg::mapping_string (C++ function) vg::mapping_to_length (C++ function) vg::MappingQualityMethod (C++ type) vg::maps_to_node (C++ function) vg::MaximalExactMatch (C++ class) vg::MaximalExactMatch::begin (C++ member) vg::MaximalExactMatch::end (C++ member) vg::MaximalExactMatch::fill_match_count (C++ function) vg::MaximalExactMatch::fill_nodes (C++ function) vg::MaximalExactMatch::length (C++ function) vg::MaximalExactMatch::match_count (C++ member) vg::MaximalExactMatch::MaximalExactMatch (C++ function) vg::MaximalExactMatch::nodes (C++ member) vg::MaximalExactMatch::range (C++ member) vg::MaximalExactMatch::sequence (C++ function) vg::median (C++ function) vg::mems_to_json (C++ function) vg::merge_alignments (C++ function), [1] vg::mergeNodeObjects (C++ function) vg::minSup (C++ function) vg::multinomial_sampling_prob_ln (C++ function) vg::NestedSite (C++ class) vg::NestedSite::child_border_index (C++ member) vg::NestedSite::children (C++ member) vg::NestedSite::edges (C++ member) vg::NestedSite::end (C++ member) vg::NestedSite::nodes (C++ member) vg::NestedSite::start (C++ member) vg::Node (C++ class) vg::Node::id (C++ member) vg::Node::name (C++ member) vg::Node::sequence (C++ member) vg::node_end (C++ function) vg::node_path_position (C++ function) vg::node_start (C++ function) vg::NodeDivider (C++ class) vg::NodeDivider::_max_id (C++ member) vg::NodeDivider::add_fragment (C++ function) vg::NodeDivider::Alt1 (C++ class) vg::NodeDivider::Alt2 (C++ class) vg::NodeDivider::break_end (C++ function) vg::NodeDivider::clear (C++ function) vg::NodeDivider::Entry (C++ class) vg::NodeDivider::Entry::alt1 (C++ member) vg::NodeDivider::Entry::alt2 (C++ member) vg::NodeDivider::Entry::Entry (C++ function) vg::NodeDivider::Entry::operator[] (C++ function) vg::NodeDivider::Entry::ref (C++ member) vg::NodeDivider::Entry::sup (C++ function) vg::NodeDivider::Entry::sup_alt1 (C++ member) vg::NodeDivider::Entry::sup_alt2 (C++ member) vg::NodeDivider::Entry::sup_ref (C++ member) vg::NodeDivider::EntryCat (C++ type) vg::NodeDivider::index (C++ member) vg::NodeDivider::Last (C++ class) vg::NodeDivider::map_node (C++ function) vg::NodeDivider::NodeHash (C++ type) vg::NodeDivider::NodeMap (C++ type) vg::NodeDivider::Ref (C++ class) vg::NodePileup (C++ class) vg::NodePileup::base_pileup (C++ member) vg::NodePileup::node_id (C++ member) vg::NodeSide (C++ class) vg::NodeSide::flip (C++ function) vg::NodeSide::is_end (C++ member) vg::NodeSide::node (C++ member) vg::NodeSide::NodeSide (C++ function), [1] vg::NodeSide::operator!= (C++ function) vg::NodeSide::operator< (C++ function) vg::NodeSide::operator== (C++ function) vg::NodeSide::pair_from_edge (C++ function), [1] vg::NodeSide::pair_from_end_edge (C++ function) vg::NodeSide::pair_from_start_edge (C++ function) vg::NodeTraversal (C++ class) vg::NodeTraversal::backward (C++ member) vg::NodeTraversal::node (C++ member) vg::NodeTraversal::NodeTraversal (C++ function), [1] vg::NodeTraversal::operator!= (C++ function) vg::NodeTraversal::operator< (C++ function) vg::NodeTraversal::operator== (C++ function) vg::NodeTraversal::reverse (C++ function) vg::nonATGCNtoN (C++ function) vg::None (C++ class) vg::off_t (C++ type) vg::offset (C++ function) vg::operator< (C++ function) vg::operator<< (C++ function), [1], [2], [3], [4], [5], [6] vg::operator== (C++ function), [1] vg::overlap (C++ function) vg::pair_hash_map (C++ class) vg::pair_hash_map::pair_hash_map (C++ function) vg::parse_bed_regions (C++ function) vg::parse_region (C++ function), [1], [2] vg::parse_rg_sample_map (C++ function) vg::Path (C++ class) vg::Path::is_circular (C++ member) vg::Path::length (C++ member) vg::Path::mapping (C++ member) vg::Path::name (C++ member) vg::path_end (C++ function) vg::path_from_length (C++ function) vg::path_from_node_traversals (C++ function) vg::path_is_simple_match (C++ function) vg::path_start (C++ function) vg::path_to_length (C++ function) vg::path_to_string (C++ function) vg::Paths (C++ class) vg::Paths::_paths (C++ member) vg::Paths::all_path_names (C++ function) vg::Paths::append (C++ function), [1] vg::Paths::append_mapping (C++ function), [1] vg::Paths::are_consecutive_nodes_in_path (C++ function) vg::Paths::circular (C++ member) vg::Paths::clear (C++ function) vg::Paths::clear_mapping_ranks (C++ function) vg::Paths::compact_ranks (C++ function) vg::Paths::create_path (C++ function) vg::Paths::divide_mapping (C++ function), [1] vg::Paths::empty (C++ function) vg::Paths::extend (C++ function), [1] vg::Paths::find_mapping (C++ function) vg::Paths::for_each (C++ function) vg::Paths::for_each_mapping (C++ function) vg::Paths::for_each_name (C++ function) vg::Paths::for_each_stream (C++ function) vg::Paths::get_create_path (C++ function) vg::Paths::get_next_rank (C++ function) vg::Paths::get_node_mapping (C++ function), [1] vg::Paths::get_node_mapping_copies_by_rank (C++ function) vg::Paths::get_node_mappings_by_rank (C++ function) vg::Paths::get_path (C++ function) vg::Paths::has_mapping (C++ function) vg::Paths::has_node_mapping (C++ function), [1] vg::Paths::has_path (C++ function) vg::Paths::head_tail_nodes (C++ member) vg::Paths::increment_node_ids (C++ function) vg::Paths::insert_mapping (C++ function) vg::Paths::is_head_or_tail_node (C++ function) vg::Paths::keep_paths (C++ function) vg::Paths::load (C++ function) vg::Paths::make_circular (C++ function) vg::Paths::make_linear (C++ function) vg::Paths::mapping_itr (C++ member) vg::Paths::mapping_path (C++ member) vg::Paths::mapping_path_name (C++ function) vg::Paths::mappings_by_rank (C++ member) vg::Paths::node_mapping (C++ member) vg::Paths::node_path_traversal_counts (C++ function) vg::Paths::node_path_traversals (C++ function) vg::Paths::of_node (C++ function) vg::Paths::operator= (C++ function), [1] vg::Paths::over_directed_edge (C++ function) vg::Paths::over_edge (C++ function) vg::Paths::path (C++ function) vg::Paths::Paths (C++ function), [1], [2] vg::Paths::prepend_mapping (C++ function), [1] vg::Paths::reassign_node (C++ function) vg::Paths::rebuild_mapping_aux (C++ function) vg::Paths::rebuild_node_mapping (C++ function) vg::Paths::remove_mapping (C++ function) vg::Paths::remove_node (C++ function) vg::Paths::remove_path (C++ function) vg::Paths::remove_paths (C++ function) vg::Paths::replace_mapping (C++ function) vg::Paths::size (C++ function) vg::Paths::sort_by_mapping_rank (C++ function) vg::Paths::swap_node_ids (C++ function) vg::Paths::to_graph (C++ function) vg::Paths::to_json (C++ function) vg::Paths::traverse_left (C++ function) vg::Paths::traverse_right (C++ function) vg::Paths::write (C++ function) vg::paths_from_graph (C++ function) vg::phred_to_logprob (C++ function) vg::phred_to_prob (C++ function) vg::Pictographs (C++ class) vg::Pictographs::count (C++ member) vg::Pictographs::hashed (C++ function) vg::Pictographs::Pictographs (C++ function), [1] vg::Pictographs::random (C++ function) vg::Pictographs::rng (C++ member) vg::Pictographs::symbols (C++ member) vg::Pictographs::~Pictographs (C++ function) vg::Pileup (C++ class) vg::Pileup::edge_pileups (C++ member) vg::Pileup::node_pileups (C++ member) vg::Pileups (C++ class) vg::Pileups::_bases_count (C++ member) vg::Pileups::_edge_pileups (C++ member) vg::Pileups::_graph (C++ member) vg::Pileups::_max_depth (C++ member) vg::Pileups::_max_mismatch_count (C++ member) vg::Pileups::_max_mismatches (C++ member) vg::Pileups::_min_quality (C++ member) vg::Pileups::_min_quality_count (C++ member) vg::Pileups::_node_pileups (C++ member) vg::Pileups::_use_mapq (C++ member) vg::Pileups::_window_size (C++ member) vg::Pileups::base_equal (C++ function) vg::Pileups::casify (C++ function) vg::Pileups::clear (C++ function) vg::Pileups::combined_quality (C++ function) vg::Pileups::compute_from_alignment (C++ function) vg::Pileups::compute_from_edit (C++ function) vg::Pileups::count_mismatches (C++ function) vg::Pileups::EdgePileupHash (C++ type) vg::Pileups::extend (C++ function) vg::Pileups::extract (C++ function) vg::Pileups::extract_match (C++ function) vg::Pileups::for_each_edge_pileup (C++ function) vg::Pileups::for_each_node_pileup (C++ function) vg::Pileups::get_base_pileup (C++ function), [1] vg::Pileups::get_create_base_pileup (C++ function) vg::Pileups::get_create_edge_pileup (C++ function) vg::Pileups::get_create_node_pileup (C++ function) vg::Pileups::get_edge_pileup (C++ function) vg::Pileups::get_node_pileup (C++ function) vg::Pileups::insert_edge_pileup (C++ function) vg::Pileups::insert_node_pileup (C++ function) vg::Pileups::load (C++ function) vg::Pileups::make_delete (C++ function), [1] vg::Pileups::make_insert (C++ function) vg::Pileups::make_match (C++ function) vg::Pileups::merge (C++ function) vg::Pileups::merge_base_pileups (C++ function) vg::Pileups::merge_edge_pileups (C++ function) vg::Pileups::merge_node_pileups (C++ function) vg::Pileups::NodePileupHash (C++ type) vg::Pileups::operator= (C++ function), [1] vg::Pileups::parse_base_offsets (C++ function) vg::Pileups::parse_delete (C++ function) vg::Pileups::parse_insert (C++ function) vg::Pileups::pass_filter (C++ function) vg::Pileups::Pileups (C++ function), [1], [2] vg::Pileups::to_json (C++ function) vg::Pileups::write (C++ function) vg::Pileups::~Pileups (C++ function) vg::pmax (C++ function) vg::pos_t (C++ type) vg::Position (C++ class) vg::Position::is_reverse (C++ member) vg::Position::node_id (C++ member) vg::Position::offset (C++ member) vg::pow_ln (C++ function) vg::prob_to_logprob (C++ function) vg::prob_to_phred (C++ function) vg::Progressive (C++ class) vg::Progressive::create_progress (C++ function), [1] vg::Progressive::destroy_progress (C++ function) vg::Progressive::increment_progress (C++ function) vg::Progressive::last_progress (C++ member) vg::Progressive::preload_progress (C++ function) vg::Progressive::progress (C++ member) vg::Progressive::progress_count (C++ member) vg::Progressive::progress_message (C++ member) vg::Progressive::progress_seen (C++ member) vg::Progressive::show_progress (C++ member) vg::Progressive::update_progress (C++ function) vg::QualAdjAligner (C++ class) vg::QualAdjAligner::adjusted_score_matrix (C++ member) vg::QualAdjAligner::align_pinned (C++ function) vg::QualAdjAligner::max_qual_score (C++ member) vg::QualAdjAligner::scaled_gap_extension (C++ member) vg::QualAdjAligner::scaled_gap_open (C++ member) vg::quality_char_to_short (C++ function) vg::quality_short_to_char (C++ function) vg::ReadFilter (C++ class) vg::ReadFilter::context_size (C++ member) vg::ReadFilter::Counts (C++ class) vg::ReadFilter::Counts::Counts (C++ function) vg::ReadFilter::Counts::defray (C++ member) vg::ReadFilter::Counts::filtered (C++ member) vg::ReadFilter::Counts::max_overhang (C++ member) vg::ReadFilter::Counts::min_mapq (C++ member) vg::ReadFilter::Counts::min_score (C++ member) vg::ReadFilter::Counts::operator+= (C++ function) vg::ReadFilter::Counts::read (C++ member) vg::ReadFilter::Counts::repeat (C++ member) vg::ReadFilter::Counts::split (C++ member) vg::ReadFilter::defray_count (C++ member) vg::ReadFilter::defray_length (C++ member) vg::ReadFilter::drop_split (C++ member) vg::ReadFilter::filter (C++ function) vg::ReadFilter::frac_score (C++ member) vg::ReadFilter::has_repeat (C++ function) vg::ReadFilter::is_split (C++ function) vg::ReadFilter::max_overhang (C++ member) vg::ReadFilter::min_mapq (C++ member) vg::ReadFilter::min_primary (C++ member) vg::ReadFilter::min_secondary (C++ member) vg::ReadFilter::outbase (C++ member) vg::ReadFilter::regions_file (C++ member) vg::ReadFilter::repeat_size (C++ member) vg::ReadFilter::sub_score (C++ member) vg::ReadFilter::threads (C++ member) vg::ReadFilter::trim_ambiguous_end (C++ function) vg::ReadFilter::trim_ambiguous_ends (C++ function) vg::ReadFilter::verbose (C++ member) vg::Realigner (C++ class) vg::Realigner::construct (C++ function) vg::Realigner::debug (C++ member) vg::Realigner::doubling_steps (C++ member) vg::Realigner::edge_max (C++ member) vg::Realigner::end_pos (C++ member) vg::Realigner::gcsaidx (C++ member) vg::Realigner::identity_trigger (C++ member) vg::Realigner::idx_kmer_size (C++ member) vg::Realigner::idx_path_only (C++ member) vg::Realigner::lcpidx (C++ member) vg::Realigner::mapper (C++ member) vg::Realigner::realign (C++ function) vg::Realigner::realign_unpaired (C++ member) vg::Realigner::Realigner (C++ function) vg::Realigner::ref (C++ member) vg::Realigner::seq_name (C++ member) vg::Realigner::softclip_trigger (C++ member) vg::Realigner::start_pos (C++ member) vg::Realigner::target (C++ member) vg::Realigner::vcf_file (C++ member) vg::Realigner::xgidx (C++ member) vg::ReferenceIndex (C++ class) vg::ReferenceIndex::byId (C++ member) vg::ReferenceIndex::byStart (C++ member) vg::ReferenceIndex::ReferenceIndex (C++ function) vg::ReferenceIndex::sequence (C++ member) vg::Region (C++ class) vg::Region::end (C++ member) vg::Region::seq (C++ member) vg::Region::start (C++ member) vg::reverse (C++ function), [1] vg::reverse_complement (C++ function), [1] vg::reverse_complement_alignment (C++ function) vg::reverse_complement_alignments (C++ function) vg::reverse_complement_edit (C++ function) vg::reverse_complement_mapping (C++ function) vg::reverse_complement_path (C++ function) vg::sam_flag (C++ function) vg::Sampler (C++ class) vg::Sampler::alignment (C++ function) vg::Sampler::alignment_pair (C++ function) vg::Sampler::alignment_seq (C++ function) vg::Sampler::alignment_with_error (C++ function) vg::Sampler::forward_only (C++ member) vg::Sampler::mutate (C++ function) vg::Sampler::mutate_edit (C++ function) vg::Sampler::next_pos_chars (C++ function) vg::Sampler::node_cache (C++ member) vg::Sampler::node_length (C++ function) vg::Sampler::nonce (C++ member) vg::Sampler::pos_char (C++ function) vg::Sampler::position (C++ function) vg::Sampler::rng (C++ member) vg::Sampler::Sampler (C++ function) vg::Sampler::sequence (C++ function) vg::Sampler::xgidx (C++ member) vg::SB_Input (C++ class) vg::SB_Input::edges (C++ member) vg::SB_Input::num_vertices (C++ member) vg::set_intersection (C++ function) vg::sha1head (C++ function) vg::sha1sum (C++ function) vg::Side2Component (C++ type) vg::SideSet (C++ type) vg::simplify (C++ function), [1], [2] vg::SiteFinder (C++ class) vg::SiteFinder::for_each_site_parallel (C++ function) vg::SiteFinder::~SiteFinder (C++ function) vg::SiteTraversal (C++ class) vg::SiteTraversal::Visit (C++ class) vg::SiteTraversal::Visit::backward (C++ member) vg::SiteTraversal::Visit::child (C++ member) vg::SiteTraversal::Visit::node (C++ member) vg::SiteTraversal::Visit::Visit (C++ function), [1], [2] vg::SiteTraversal::visits (C++ member) vg::softclip_end (C++ function), [1] vg::softclip_start (C++ function), [1] vg::split_delims (C++ function), [1] vg::SSWAligner (C++ class) vg::SSWAligner::align (C++ function) vg::SSWAligner::gap_extension (C++ member) vg::SSWAligner::gap_open (C++ member) vg::SSWAligner::match (C++ member) vg::SSWAligner::mismatch (C++ member) vg::SSWAligner::PrintAlignment (C++ function) vg::SSWAligner::ssw_to_vg (C++ function) vg::SSWAligner::SSWAligner (C++ function) vg::SSWAligner::~SSWAligner (C++ function) vg::stdev (C++ function), [1] vg::StrandSupport (C++ class) vg::StrandSupport::depth (C++ function) vg::StrandSupport::fs (C++ member) vg::StrandSupport::likelihood (C++ member) vg::StrandSupport::operator+= (C++ function) vg::StrandSupport::operator- (C++ function) vg::StrandSupport::operator< (C++ function) vg::StrandSupport::operator== (C++ function) vg::StrandSupport::operator>= (C++ function) vg::StrandSupport::os (C++ member) vg::StrandSupport::rs (C++ member) vg::StrandSupport::StrandSupport (C++ function) vg::StrandSupport::total (C++ function) vg::string_hash_map (C++ class) vg::string_hash_map::string_hash_map (C++ function) vg::string_quality_char_to_short (C++ function) vg::string_quality_short_to_char (C++ function) vg::strip_from_end (C++ function) vg::strip_from_start (C++ function) vg::subcommand (C++ type) vg::subcommand::Subcommand (C++ class) vg::subcommand::Subcommand::description (C++ member) vg::subcommand::Subcommand::for_each (C++ function) vg::subcommand::Subcommand::get (C++ function) vg::subcommand::Subcommand::get_description (C++ function) vg::subcommand::Subcommand::get_main (C++ function) vg::subcommand::Subcommand::get_name (C++ function) vg::subcommand::Subcommand::get_registry (C++ function) vg::subcommand::Subcommand::main_function (C++ member) vg::subcommand::Subcommand::name (C++ member) vg::subcommand::Subcommand::operator() (C++ function) vg::subcommand::Subcommand::Subcommand (C++ function) vg::sum (C++ function) vg::SuperBubble (C++ class) vg::SuperBubble::end_node (C++ member) vg::SuperBubble::isNested (C++ member) vg::SuperBubble::level_to_nodes (C++ member) vg::SuperBubble::start_node (C++ member) vg::superbubbles (C++ function) vg::Support (C++ class) vg::Support::forward (C++ member) vg::Support::left (C++ member) vg::Support::quality (C++ member) vg::Support::reverse (C++ member) vg::Support::right (C++ member) vg::tmpfilename (C++ function) vg::to_length (C++ function) vg::to_length_after_pos (C++ function) vg::to_length_before_pos (C++ function) vg::translate_nodes (C++ function) vg::Translation (C++ class) vg::Translation::from (C++ member) vg::Translation::to (C++ member) vg::Translator (C++ class) vg::Translator::build_position_table (C++ function) vg::Translator::get_translation (C++ function) vg::Translator::load (C++ function) vg::Translator::overlay (C++ function) vg::Translator::pos_to_trans (C++ member) vg::Translator::translate (C++ function), [1], [2], [3], [4], [5] vg::Translator::translations (C++ member) vg::Translator::Translator (C++ function), [1], [2] vg::TraversalFinder (C++ class) vg::TraversalFinder::find_traversals (C++ function) vg::TraversalFinder::~TraversalFinder (C++ function) vg::TraversalSupportCalculator (C++ class) vg::TraversalSupportCalculator::calculate_supports (C++ function) vg::TraversalSupportCalculator::~TraversalSupportCalculator (C++ function) vg::Tree (C++ class) vg::Tree::for_each_postorder (C++ function) vg::Tree::for_each_preorder (C++ function) vg::Tree::Node (C++ type) vg::Tree::root (C++ member) vg::Tree::Tree (C++ function) vg::Tree::~Tree (C++ function) vg::TreeNode (C++ class) vg::TreeNode::children (C++ member) vg::TreeNode::for_each_postorder (C++ function) vg::TreeNode::for_each_preorder (C++ function) vg::TreeNode::parent (C++ member) vg::TreeNode::TreeNode (C++ function) vg::TreeNode::v (C++ member) vg::TreeNode::~TreeNode (C++ function) vg::trim_alignment (C++ function) vg::trim_hanging_ends (C++ function) vg::triple_to_vg (C++ function) vg::TrivialTraversalFinder (C++ class) vg::TrivialTraversalFinder::find_traversals (C++ function) vg::TrivialTraversalFinder::graph (C++ member) vg::TrivialTraversalFinder::TrivialTraversalFinder (C++ function) vg::TrivialTraversalFinder::~TrivialTraversalFinder (C++ function) vg::ultrabubble_recurse (C++ function) vg::ultrabubble_tree (C++ function) vg::ultrabubbles (C++ function) vg::unittest (C++ type) vg::unittest::run_unit_tests (C++ function) vg::VcfBuffer (C++ class) vg::VcfBuffer::buffer (C++ member) vg::VcfBuffer::file (C++ member) vg::VcfBuffer::fill_buffer (C++ function) vg::VcfBuffer::get (C++ function) vg::VcfBuffer::handle_buffer (C++ function) vg::VcfBuffer::has_buffer (C++ member) vg::VcfBuffer::has_tabix (C++ function) vg::VcfBuffer::operator= (C++ function) vg::VcfBuffer::safe_to_get (C++ member) vg::VcfBuffer::set_region (C++ function) vg::VcfBuffer::VcfBuffer (C++ function), [1] vg::VcfRecordConverter (C++ class) vg::VcfRecordConverter::convert (C++ function) vg::VcfRecordConverter::~VcfRecordConverter (C++ function) vg::VcfRecordFilter (C++ class) vg::VcfRecordFilter::accept_record (C++ function) vg::VcfRecordFilter::~VcfRecordFilter (C++ function) vg::VG (C++ class) vg::VG::_for_each_kmer (C++ function) vg::VG::add_edge (C++ function) vg::VG::add_edges (C++ function), [1], [2] vg::VG::add_node (C++ function) vg::VG::add_nodes (C++ function), [1] vg::VG::add_nodes_and_edges (C++ function) vg::VG::add_start_end_markers (C++ function) vg::VG::adjacent (C++ function) vg::VG::align (C++ function), [1], [2], [3], [4] vg::VG::align_qual_adjusted (C++ function), [1] vg::VG::append (C++ function) vg::VG::backtracking_unroll (C++ function) vg::VG::bluntify (C++ function) vg::VG::break_cycles (C++ function) vg::VG::build_edge_indexes (C++ function) vg::VG::build_gcsa_lcp (C++ function) vg::VG::build_indexes (C++ function) vg::VG::build_node_indexes (C++ function) vg::VG::circularize (C++ function), [1] vg::VG::clear_edge_indexes (C++ function) vg::VG::clear_edge_indexes_no_resize (C++ function) vg::VG::clear_indexes (C++ function) vg::VG::clear_indexes_no_resize (C++ function) vg::VG::clear_node_indexes (C++ function) vg::VG::clear_node_indexes_no_resize (C++ function) vg::VG::clear_paths (C++ function) vg::VG::collect_subgraph (C++ function) vg::VG::combine (C++ function) vg::VG::common_ancestor_next (C++ function) vg::VG::common_ancestor_prev (C++ function) vg::VG::compact_ids (C++ function) vg::VG::concat_mappings_for_node_pair (C++ function) vg::VG::concat_mappings_for_nodes (C++ function) vg::VG::concat_nodes (C++ function) vg::VG::connect_node_to_nodes (C++ function), [1] vg::VG::connect_nodes_to_node (C++ function), [1] vg::VG::create_edge (C++ function), [1], [2], [3] vg::VG::create_node (C++ function) vg::VG::create_path (C++ function), [1] vg::VG::current_id (C++ member) vg::VG::dagify (C++ function) vg::VG::decrement_node_ids (C++ function) vg::VG::destroy_edge (C++ function), [1], [2] vg::VG::destroy_node (C++ function), [1] vg::VG::dfs (C++ function), [1], [2] vg::VG::dice_nodes (C++ function) vg::VG::disjoint_subgraphs (C++ function) vg::VG::distance_to_head (C++ function), [1] vg::VG::distance_to_tail (C++ function), [1], [2] vg::VG::divide_node (C++ function), [1] vg::VG::divide_path (C++ function) vg::VG::edge_by_sides (C++ member) vg::VG::edge_count (C++ function) vg::VG::edge_index (C++ member) vg::VG::edges_end (C++ function), [1] vg::VG::edges_from (C++ function) vg::VG::edges_of (C++ function) vg::VG::edges_of_node (C++ function) vg::VG::edges_of_nodes (C++ function) vg::VG::edges_on_end (C++ member) vg::VG::edges_on_start (C++ member) vg::VG::edges_start (C++ function), [1] vg::VG::edges_to (C++ function) vg::VG::edit (C++ function) vg::VG::elementary_cycles (C++ function) vg::VG::empty (C++ function) vg::VG::empty_edge_ends (C++ member) vg::VG::empty_ids (C++ member) vg::VG::end_degree (C++ function) vg::VG::ensure_breakpoints (C++ function) vg::VG::expand_context (C++ function) vg::VG::expand_path (C++ function), [1] vg::VG::extend (C++ function), [1] vg::VG::fill_empty_path_mappings (C++ function) vg::VG::find_breakpoints (C++ function) vg::VG::find_node_by_name_or_add_new (C++ function) vg::VG::flip_doubly_reversed_edges (C++ function) vg::VG::for_each_connected_node (C++ function) vg::VG::for_each_edge (C++ function) vg::VG::for_each_edge_parallel (C++ function) vg::VG::for_each_gcsa_kmer_position_parallel (C++ function) vg::VG::for_each_kmer (C++ function) vg::VG::for_each_kmer_of_node (C++ function) vg::VG::for_each_kmer_parallel (C++ function) vg::VG::for_each_kpath (C++ function), [1] vg::VG::for_each_kpath_of_node (C++ function), [1] vg::VG::for_each_kpath_parallel (C++ function), [1] vg::VG::for_each_node (C++ function) vg::VG::for_each_node_parallel (C++ function) vg::VG::force_path_match (C++ function) vg::VG::forwardize_breakpoints (C++ function) vg::VG::from_gfa (C++ function) vg::VG::from_turtle (C++ function) vg::VG::full_siblings_from (C++ function) vg::VG::full_siblings_to (C++ function) vg::VG::gcsa_handle_node_in_graph (C++ function) vg::VG::get_edge (C++ function), [1], [2] vg::VG::get_gcsa_kmers (C++ function) vg::VG::get_node (C++ function) vg::VG::get_node_at_nucleotide (C++ function) vg::VG::get_node_id_to_variant (C++ function) vg::VG::get_superbubbles (C++ function), [1] vg::VG::graph (C++ member) vg::VG::has_edge (C++ function), [1], [2], [3] vg::VG::has_inverting_edge (C++ function) vg::VG::has_inverting_edge_from (C++ function) vg::VG::has_inverting_edge_to (C++ function) vg::VG::has_inverting_edges (C++ function) vg::VG::has_node (C++ function), [1], [2] vg::VG::hash (C++ function) vg::VG::head_nodes (C++ function), [1] vg::VG::identically_oriented_sibling_sets (C++ function) vg::VG::include (C++ function) vg::VG::increment_node_ids (C++ function) vg::VG::index_edge_by_node_sides (C++ function) vg::VG::index_paths (C++ function) vg::VG::init (C++ function) vg::VG::is_acyclic (C++ function) vg::VG::is_ancestor_next (C++ function), [1] vg::VG::is_ancestor_prev (C++ function), [1] vg::VG::is_head_node (C++ function), [1] vg::VG::is_self_looping (C++ function) vg::VG::is_tail_node (C++ function), [1] vg::VG::is_valid (C++ function) vg::VG::join_heads (C++ function), [1] vg::VG::join_tails (C++ function) vg::VG::keep_multinode_strongly_connected_components (C++ function) vg::VG::keep_path (C++ function) vg::VG::keep_paths (C++ function) vg::VG::kmer_context (C++ function) vg::VG::kpaths (C++ function), [1] vg::VG::kpaths_of_node (C++ function), [1], [2] vg::VG::left_degree (C++ function) vg::VG::length (C++ function) vg::VG::likelihoods (C++ function) vg::VG::make_translation (C++ function) vg::VG::mapping_is_total_match (C++ function) vg::VG::max_node_id (C++ function) vg::VG::merge (C++ function), [1] vg::VG::merge_nodes (C++ function) vg::VG::merge_union (C++ function) vg::VG::min_node_id (C++ function) vg::VG::multinode_strongly_connected_components (C++ function) vg::VG::name (C++ member) vg::VG::next_kpaths_from_node (C++ function) vg::VG::node_by_id (C++ member) vg::VG::node_count (C++ function) vg::VG::node_count_next (C++ function) vg::VG::node_count_prev (C++ function) vg::VG::node_index (C++ member) vg::VG::node_rank (C++ function), [1] vg::VG::node_starts_in_path (C++ function), [1] vg::VG::nodes_are_perfect_path_neighbors (C++ function) vg::VG::nodes_next (C++ function), [1] vg::VG::nodes_prev (C++ function), [1] vg::VG::nonoverlapping_node_context_without_paths (C++ function) vg::VG::normalize (C++ function) vg::VG::operator= (C++ function), [1] vg::VG::orient_nodes_forward (C++ function) vg::VG::overlay_node_translations (C++ function) vg::VG::path_edge_count (C++ function) vg::VG::path_end_node_offset (C++ function) vg::VG::path_identity (C++ function) vg::VG::path_sequence (C++ function) vg::VG::path_string (C++ function), [1] vg::VG::paths (C++ member) vg::VG::paths_as_alignments (C++ function) vg::VG::paths_between (C++ function), [1] vg::VG::Plan (C++ class) vg::VG::Plan::alleles (C++ member) vg::VG::Plan::graph (C++ member) vg::VG::Plan::name (C++ member) vg::VG::Plan::phase_visits (C++ member) vg::VG::Plan::Plan (C++ function) vg::VG::Plan::seq (C++ member) vg::VG::Plan::variant_alts (C++ member) vg::VG::prev_kpaths_from_node (C++ function) vg::VG::print_edges (C++ function) vg::VG::prune_complex (C++ function) vg::VG::prune_complex_paths (C++ function) vg::VG::prune_complex_with_head_tail (C++ function) vg::VG::prune_short_subgraphs (C++ function) vg::VG::random_read (C++ function) vg::VG::rebuild_edge_indexes (C++ function) vg::VG::rebuild_indexes (C++ function) vg::VG::remove_duplicated_in (C++ function) vg::VG::remove_duplicates (C++ function) vg::VG::remove_inverting_edges (C++ function) vg::VG::remove_node_forwarding_edges (C++ function) vg::VG::remove_non_path (C++ function) vg::VG::remove_null_nodes (C++ function) vg::VG::remove_null_nodes_forwarding_edges (C++ function) vg::VG::remove_orphan_edges (C++ function) vg::VG::resize_indexes (C++ function) vg::VG::right_degree (C++ function) vg::VG::same_context (C++ function) vg::VG::serialize_to_file (C++ function) vg::VG::serialize_to_ostream (C++ function) vg::VG::set_edge (C++ function) vg::VG::siblings_from (C++ function) vg::VG::siblings_of (C++ function) vg::VG::siblings_to (C++ function) vg::VG::sides_context (C++ function) vg::VG::sides_from (C++ function), [1] vg::VG::sides_of (C++ function) vg::VG::sides_to (C++ function), [1] vg::VG::simple_components (C++ function) vg::VG::simple_multinode_components (C++ function) vg::VG::simplify_from_siblings (C++ function) vg::VG::simplify_siblings (C++ function) vg::VG::simplify_to_siblings (C++ function) vg::VG::size (C++ function) vg::VG::sort (C++ function) vg::VG::start_degree (C++ function) vg::VG::strongly_connected_components (C++ function) vg::VG::swap_node_id (C++ function), [1] vg::VG::swap_nodes (C++ function) vg::VG::sync_paths (C++ function) vg::VG::tail_nodes (C++ function), [1] vg::VG::to_dot (C++ function), [1] vg::VG::to_gfa (C++ function) vg::VG::to_turtle (C++ function) vg::VG::topological_sort (C++ function) vg::VG::total_length_of_nodes (C++ function) vg::VG::transitive_sibling_sets (C++ function) vg::VG::trav_sequence (C++ function) vg::VG::travs_from (C++ function) vg::VG::travs_of (C++ function) vg::VG::travs_to (C++ function) vg::VG::unchop (C++ function) vg::VG::unfold (C++ function) vg::VG::unindex_edge_by_node_sides (C++ function), [1] vg::VG::VG (C++ function), [1], [2], [3], [4], [5] vg::VG::vg_to_sb_input (C++ function) vg::VG::wrap_with_null_nodes (C++ function) vg::VG::write_gcsa_kmers (C++ function) vg::VG::write_gcsa_kmers_to_tmpfile (C++ function) vg::VG::~VG (C++ function) vg::vg_to_cactus (C++ function) vg::vg_to_sb_input (C++ function) vg::VG_VERSION_STRING (C++ member) vg::VGset (C++ class) vg::VGset::filenames (C++ member) vg::VGset::for_each (C++ function) vg::VGset::for_each_gcsa_kmer_position_parallel (C++ function) vg::VGset::for_each_kmer_parallel (C++ function) vg::VGset::get_gcsa_kmers (C++ function) vg::VGset::index_kmers (C++ function) vg::VGset::merge_id_space (C++ function) vg::VGset::show_progress (C++ member) vg::VGset::store_in_index (C++ function) vg::VGset::store_paths_in_index (C++ function) vg::VGset::to_xg (C++ function), [1] vg::VGset::transform (C++ function) vg::VGset::VGset (C++ function), [1] vg::VGset::write_gcsa_kmers_binary (C++ function), [1] vg::VGset::write_gcsa_out (C++ function) vg::vpmax (C++ function) vg::wrap_text (C++ function) vg::write_alignment_to_file (C++ function), [1] vg::write_alignments (C++ function) vg::xg_cached_next_pos_chars (C++ function) vg::xg_cached_node_length (C++ function) vg::xg_cached_pos_char (C++ function) VG_GIT_VERSION (C macro) vg_help (C++ function)