Index

_

_CONVERT (C macro), [1] _field2json (C++ function) _json2field (C++ function)

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

A

add_thread_edges_to_set (C++ function), [1] add_thread_nodes_to_set (C++ function), [1] add_trivial_edits (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::score_exact_match (C++ function), [1], [2], [3], [4] AlnSorter (C++ class) AlnSorter::invert (C++ member) AlnSorter::mycomparison (C++ function) AlnSorter::operator() (C++ function) alnsortkey (C++ member) augment_with_pileups (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_empty_prefix (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_empty_alignment (C++ function) BandedGlobalAligner::AltTracebackStack::next_is_empty (C++ function) BandedGlobalAligner::AltTracebackStack::next_traceback_alignment (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) BaseAligner::compute_mapping_quality (C++ function), [1] BaseAligner::compute_paired_mapping_quality (C++ function) BaseAligner::create_gssw_graph (C++ function) BaseAligner::estimate_max_possible_mapping_quality (C++ function) BaseAligner::estimate_next_best_score (C++ function) BaseAligner::graph_cigar (C++ function) BaseAligner::gssw_mapping_to_alignment (C++ function) BaseAligner::init_mapping_quality (C++ function) BaseAligner::longest_detectable_gap (C++ function), [1] BaseAligner::mapping_quality_score_diff (C++ function) BaseAligner::max_possible_mapping_quality (C++ function) BaseAligner::maximum_mapping_quality_approx (C++ function) BaseAligner::maximum_mapping_quality_exact (C++ function) BaseAligner::remove_bonuses (C++ function) BaseAligner::reverse_graph (C++ function) BaseAligner::score_gap (C++ function) BaseAligner::score_gappy_alignment (C++ function) BaseAligner::score_to_unnormalized_likelihood_ln (C++ function) BaseAligner::score_ungapped_alignment (C++ function) BaseAligner::unreverse_graph (C++ function) BaseAligner::unreverse_graph_mapping (C++ function) BaseAligner::~BaseAligner (C++ function) bin2hex (C++ function)

C

CATCH_CONFIG_RUNNER (C macro) compute_pileups (C++ function) construct_graph_from_nodes_and_edges (C++ function), [1]

custom_aln_sort_key (C++ class) custom_aln_sort_key::operator() (C++ function) custom_pos_sort_key (C++ class) custom_pos_sort_key::operator() (C++ function)

E

exp_overflow_limit (C++ member)

G

GAMSorter::dumb_sort (C++ function) GAMSorter::equal_to (C++ function) GAMSorter::get_min_position (C++ function), [1] GAMSorter::greater_than (C++ function) GAMSorter::less_than (C++ function) GAMSorter::min_aln_first (C++ function) GAMSorter::paired_sort (C++ function) GAMSorter::sort (C++ function)

GAMSorter::stream_sort (C++ function) GAMSorter::write_index (C++ function) GAMSorter::write_temp (C++ function) gbwt_to_thread_mapping (C++ function) gfak (C++ type) google (C++ type) google::protobuf (C++ type) GPBWT_MODE (C macro)

H

help_add (C++ function) help_align (C++ function) help_annotate (C++ function) help_augment (C++ function) help_benchmark (C++ function) help_bugs (C++ function) help_call (C++ function) help_chunk (C++ function) help_circularize (C++ function) help_compare (C++ function) help_concat (C++ function) help_construct (C++ function) help_deconstruct (C++ function) help_explode (C++ function) help_filter (C++ function) help_find (C++ function) help_gamsort (C++ function) help_genotype (C++ function) help_help (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_mpmap (C++ function) help_msga (C++ function) help_pack (C++ function) help_paths (C++ function) help_sift (C++ function) help_sim (C++ function) help_simplify (C++ function) help_snarl (C++ function) help_sort (C++ function) help_srpe (C++ function) help_stats (C++ function) help_surject (C++ function) help_trace (C++ function) help_translate (C++ function) help_validate (C++ function) help_vectorize (C++ function) help_version (C++ function) help_view (C++ function) help_xg (C++ function) hex2bin (C++ function) Homogenizer::cut_nonref_tips (C++ function) Homogenizer::cut_tips (C++ function), [1] Homogenizer::find_non_ref_tips (C++ function) Homogenizer::find_tips (C++ function) Homogenizer::homogenize (C++ function), [1]

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)

L

list_haplotypes (C++ function), [1]

M

main (C++ function) main_add (C++ function) main_align (C++ function) main_annotate (C++ function) main_augment (C++ function) main_benchmark (C++ function) main_bugs (C++ function) main_call (C++ function) main_chunk (C++ function) main_circularize (C++ function) main_compare (C++ function) main_concat (C++ function) main_construct (C++ function) main_deconstruct (C++ function) main_explode (C++ function) main_filter (C++ function) main_find (C++ function) main_gamsort (C++ function) main_genotype (C++ function) main_help (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_mpmap (C++ function) main_msga (C++ function) main_pack (C++ function) main_paths (C++ function) main_sift (C++ function) main_sim (C++ function) main_simplify (C++ function) main_snarl (C++ function) main_sort (C++ function) main_srpe (C++ function) main_stats (C++ function) main_surject (C++ function) main_test (C++ function) main_trace (C++ function) main_translate (C++ function) main_validate (C++ function) main_vectorize (C++ function) main_version (C++ function) main_view (C++ function) main_xg (C++ function) mapping_to_gbwt (C++ function) MODE_DYNAMIC (C macro) MODE_SDSL (C macro)

N

NoAlignmentInBandException::message (C++ member) NoAlignmentInBandException::what (C++ function) node_side_to_gbwt (C++ function) NodeLengthBuffer (C++ class) NodeLengthBuffer::buffer (C++ member)

NodeLengthBuffer::BUFFER_SIZE (C++ member) NodeLengthBuffer::entry_type (C++ type) NodeLengthBuffer::hash (C++ member) NodeLengthBuffer::index (C++ member) NodeLengthBuffer::NodeLengthBuffer (C++ function) NodeLengthBuffer::operator() (C++ function)

O

operator< (C++ function) operator<< (C++ function) operator== (C++ function)

output_graph_with_embedded_paths (C++ function), [1], [2], [3] output_haplotype_counts (C++ function), [1] OVERLOAD_PAIR_HASH (C macro), [1]

P

path_from_thread_t (C++ function), [1]

pb2json (C++ function), [1] possortkey (C++ member)

Q

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

QualAdjAligner::align_pinned (C++ function) QualAdjAligner::align_pinned_multi (C++ function) QualAdjAligner::QualAdjAligner (C++ function) QualAdjAligner::score_exact_match (C++ function), [1], [2] quality_scale_factor (C++ member)

S

S (C macro) sdsl (C++ type) std (C++ type) std::hash::operator() (C++ function), [1], [2], [3], [4], [5], [6] std::hash<const vg::Snarl> (C++ class) std::hash<pair<A, B>> (C++ class) std::hash<std::tuple<TT...>> (C++ class) std::hash<vg::handle_t> (C++ class) std::hash<vg::NodeSide> (C++ class) std::hash<vg::NodeTraversal> (C++ class) stream (C++ type) stream::for_each (C++ function), [1] stream::for_each_interleaved_pair_parallel (C++ function) stream::for_each_interleaved_pair_parallel_after_wait (C++ function) stream::for_each_parallel (C++ function), [1] stream::for_each_parallel_impl (C++ function) stream::MAX_PROTOBUF_SIZE (C++ member)

stream::protobuf_iterator_range (C++ function) stream::ProtobufIterator (C++ class) stream::ProtobufIterator::chunk_count (C++ member) stream::ProtobufIterator::chunk_idx (C++ member) stream::ProtobufIterator::coded_in (C++ member) stream::ProtobufIterator::get_next (C++ function) stream::ProtobufIterator::gzip_in (C++ member) stream::ProtobufIterator::handle (C++ function) stream::ProtobufIterator::has_next (C++ function) stream::ProtobufIterator::operator* (C++ function) stream::ProtobufIterator::ProtobufIterator (C++ function) stream::ProtobufIterator::raw_in (C++ member) stream::ProtobufIterator::value (C++ member) stream::ProtobufIterator::where (C++ member) stream::TARGET_PROTOBUF_SIZE (C++ member) stream::write (C++ function), [1] stream::write_buffered (C++ function) swap_remove (C++ function)

T

thread_t (C++ type), [1]

thread_to_graph_spanned (C++ function), [1] trace_haplotypes_and_paths (C++ function), [1]

U

USE_DENSE_HASH (C macro)

V

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::add_log (C++ function) vg::addArbitraryTelomerePair (C++ function) vg::adjacent_mappings (C++ function) vg::advance_split (C++ function) vg::Aligner (C++ class) vg::Aligner::~Aligner (C++ function) vg::Alignment (C++ class) vg::Alignment::correct (C++ member) vg::Alignment::discordant_insert_size (C++ member) vg::Alignment::fragment (C++ member) vg::Alignment::fragment_length_distribution (C++ member) vg::Alignment::fragment_next (C++ member) vg::Alignment::fragment_prev (C++ member) vg::Alignment::fragment_score (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::mate_mapped_to_disjoint_subgraph (C++ member) vg::Alignment::mate_on_reverse_strand (C++ member) vg::Alignment::mate_unmapped (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::read_mapped (C++ member) vg::Alignment::read_on_reverse_strand (C++ member) vg::Alignment::read_paired (C++ member) vg::Alignment::refpos (C++ member) vg::Alignment::sample_name (C++ member) vg::Alignment::score (C++ member) vg::Alignment::secondary_score (C++ member) vg::Alignment::sequence (C++ member) vg::Alignment::soft_clipped (C++ member) vg::Alignment::uniqueness (C++ member) vg::alignment_ends (C++ function) vg::alignment_from_length (C++ function) vg::alignment_middle (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::AlignmentChainModel (C++ class) vg::AlignmentChainModel::AlignmentChainModel (C++ function) vg::AlignmentChainModel::clear_scores (C++ function) vg::AlignmentChainModel::display (C++ function) vg::AlignmentChainModel::max_vertex (C++ function) vg::AlignmentChainModel::model (C++ member) vg::AlignmentChainModel::positions (C++ member) vg::AlignmentChainModel::redundant_vertexes (C++ member) vg::AlignmentChainModel::score (C++ function) vg::AlignmentChainModel::traceback (C++ function) vg::AlignmentChainModel::unaligned_bands (C++ member) vg::AlignmentChainModelVertex (C++ class) vg::AlignmentChainModelVertex::AlignmentChainModelVertex (C++ function), [1], [2] vg::AlignmentChainModelVertex::aln (C++ member) vg::AlignmentChainModelVertex::band_begin (C++ member) vg::AlignmentChainModelVertex::band_idx (C++ member) vg::AlignmentChainModelVertex::next_cost (C++ member) vg::AlignmentChainModelVertex::operator= (C++ function), [1] vg::AlignmentChainModelVertex::positions (C++ member) vg::AlignmentChainModelVertex::prev (C++ member) vg::AlignmentChainModelVertex::prev_cost (C++ member) vg::AlignmentChainModelVertex::score (C++ member) vg::AlignmentChainModelVertex::weight (C++ member) vg::AlignmentChainModelVertex::~AlignmentChainModelVertex (C++ function) vg::allATGC (C++ function) vg::allele_to_string (C++ function) vg::append_path (C++ function) vg::AppendHaplotypeCommand (C++ class) vg::AppendHaplotypeCommand::execute (C++ function) vg::AppendHaplotypeCommand::haplotype (C++ member) vg::AppendHaplotypeCommand::~AppendHaplotypeCommand (C++ function) vg::Approx (C++ class) vg::as_handle (C++ function), [1] vg::as_integer (C++ function), [1] vg::AugmentedGraph (C++ class) vg::AugmentedGraph::augment_from_alignment_edits (C++ function) vg::AugmentedGraph::base_edge (C++ function) vg::AugmentedGraph::base_graph (C++ member) vg::AugmentedGraph::clear (C++ function) vg::AugmentedGraph::graph (C++ member) vg::AugmentedGraph::is_novel_edge (C++ function) vg::AugmentedGraph::is_novel_node (C++ function) vg::AugmentedGraph::load_translations (C++ function) vg::AugmentedGraph::translator (C++ member) vg::AugmentedGraph::write_translations (C++ function) 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::empty_full_paths (C++ member) vg::BandedGlobalAligner<IntType>::AltTracebackStack::empty_score (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::BaseAligner (C++ class) vg::BaseAligner::align (C++ function) vg::BaseAligner::align_global_banded (C++ function) vg::BaseAligner::align_global_banded_multi (C++ function) vg::BaseAligner::align_pinned (C++ function) vg::BaseAligner::align_pinned_multi (C++ function) vg::BaseAligner::BaseAligner (C++ function) vg::BaseAligner::full_length_bonus (C++ member) vg::BaseAligner::gap_extension (C++ member) vg::BaseAligner::gap_open (C++ member) vg::BaseAligner::log_base (C++ member) vg::BaseAligner::match (C++ member) vg::BaseAligner::mismatch (C++ member) vg::BaseAligner::nt_table (C++ member) vg::BaseAligner::score_exact_match (C++ function), [1], [2] vg::BaseAligner::score_matrix (C++ member) vg::BaseAligner::visit_node (C++ function) vg::BaseMapper (C++ class) vg::BaseMapper::adaptive_diff_exponent (C++ member) vg::BaseMapper::adaptive_reseed_diff (C++ member) vg::BaseMapper::adaptive_reseed_length_memo (C++ member) vg::BaseMapper::adjust_alignments_for_base_quality (C++ member) vg::BaseMapper::alignment_threads (C++ member) vg::BaseMapper::assume_acyclic (C++ member) vg::BaseMapper::BaseMapper (C++ function), [1] vg::BaseMapper::check_mems (C++ function) vg::BaseMapper::clear_aligners (C++ function) vg::BaseMapper::estimate_gc_content (C++ function) vg::BaseMapper::fast_reseed (C++ member) vg::BaseMapper::fast_reseed_length_diff (C++ member) vg::BaseMapper::fill_nonredundant_sub_mem_nodes (C++ function) vg::BaseMapper::find_mems_deep (C++ function) vg::BaseMapper::find_mems_simple (C++ function) vg::BaseMapper::find_sub_mems (C++ function) vg::BaseMapper::find_sub_mems_fast (C++ function) vg::BaseMapper::first_hit_positions_by_index (C++ function) vg::BaseMapper::force_fragment_length_distr (C++ function) vg::BaseMapper::fragment_length_distr (C++ member) vg::BaseMapper::gcsa (C++ member) vg::BaseMapper::get_adaptive_min_reseed_length (C++ function) vg::BaseMapper::get_aligner (C++ function) vg::BaseMapper::get_qual_adj_aligner (C++ function) vg::BaseMapper::get_regular_aligner (C++ function) vg::BaseMapper::has_fixed_fragment_length_distr (C++ function) vg::BaseMapper::hit_max (C++ member) vg::BaseMapper::init_aligner (C++ function) vg::BaseMapper::lcp (C++ member) vg::BaseMapper::mapping_quality_method (C++ member) vg::BaseMapper::max_mapping_quality (C++ member) vg::BaseMapper::mem_positions_by_index (C++ function) vg::BaseMapper::mem_reseed_length (C++ member) vg::BaseMapper::min_mem_length (C++ member) vg::BaseMapper::next_pos_chars (C++ function) vg::BaseMapper::pos_char (C++ function) vg::BaseMapper::positions_bp_from (C++ function) vg::BaseMapper::qual_adj_aligner (C++ member) vg::BaseMapper::random_match_length (C++ function) vg::BaseMapper::regular_aligner (C++ member) vg::BaseMapper::sequence_positions (C++ function) vg::BaseMapper::set_alignment_scores (C++ function) vg::BaseMapper::set_alignment_threads (C++ function) vg::BaseMapper::set_cache_size (C++ function) vg::BaseMapper::set_fragment_length_distr_params (C++ function) vg::BaseMapper::strip_bonuses (C++ member) vg::BaseMapper::use_approx_sub_mem_count (C++ member) vg::BaseMapper::xindex (C++ member) vg::BaseMapper::~BaseMapper (C++ function) vg::BaseOption (C++ class) vg::BaseOption::BaseOption (C++ function), [1] vg::BaseOption::default_value (C++ member) vg::BaseOption::description (C++ member) vg::BaseOption::get_default_value (C++ function) vg::BaseOption::get_description (C++ function) vg::BaseOption::get_long_option (C++ function) vg::BaseOption::get_short_options (C++ function) vg::BaseOption::has_argument (C++ function) vg::BaseOption::long_opt (C++ member) vg::BaseOption::operator Value& (C++ function) vg::BaseOption::operator= (C++ function), [1] vg::BaseOption::parse (C++ function), [1] vg::BaseOption::short_opts (C++ member) vg::BaseOption::value (C++ member) vg::BaseOption::~BaseOption (C++ function) 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::benchmark_control (C++ function) vg::BenchmarkResult (C++ class) vg::BenchmarkResult::control_mean (C++ member) vg::BenchmarkResult::control_stddev (C++ member) vg::BenchmarkResult::name (C++ member) vg::BenchmarkResult::runs (C++ member) vg::BenchmarkResult::score (C++ function) vg::BenchmarkResult::score_error (C++ function) vg::BenchmarkResult::test_mean (C++ member) vg::BenchmarkResult::test_stddev (C++ member) vg::binomial_cmf_ln (C++ function) vg::BREAKPOINT (C++ class) vg::BREAKPOINT::contig (C++ member) vg::BREAKPOINT::fragl_supports (C++ member) vg::BREAKPOINT::isForward (C++ member) vg::BREAKPOINT::lower_bound (C++ member) vg::BREAKPOINT::mates (C++ member) vg::BREAKPOINT::name (C++ member) vg::BREAKPOINT::normal_supports (C++ member) vg::BREAKPOINT::other_supports (C++ member) vg::BREAKPOINT::overlap (C++ function) vg::BREAKPOINT::position (C++ member) vg::BREAKPOINT::split_supports (C++ member) vg::BREAKPOINT::start (C++ member) vg::BREAKPOINT::SV_TYPE (C++ member) vg::BREAKPOINT::to_string (C++ function) vg::BREAKPOINT::total_supports (C++ function) vg::BREAKPOINT::tumor_supports (C++ member) vg::BREAKPOINT::upper_bound (C++ member) 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::CactusSnarlFinder (C++ class) vg::CactusSnarlFinder::CactusSnarlFinder (C++ function), [1] vg::CactusSnarlFinder::find_snarls (C++ function) vg::CactusSnarlFinder::graph (C++ member) vg::CactusSnarlFinder::hint_paths (C++ member) vg::CactusSnarlFinder::recursively_emit_snarls (C++ function) vg::can_write_alleles (C++ function) vg::chain_begin (C++ function) vg::chain_begin_from (C++ function) vg::chain_end (C++ function) vg::chain_end_from (C++ function) vg::chain_rbegin (C++ function) vg::chain_rcbegin (C++ function) vg::chain_rcend (C++ function) vg::chain_rend (C++ function) vg::ChainIterator (C++ class) vg::ChainIterator::backward (C++ member) vg::ChainIterator::chain_end (C++ member) vg::ChainIterator::chain_start (C++ member) vg::ChainIterator::complement (C++ member) vg::ChainIterator::go_left (C++ member) vg::ChainIterator::is_rend (C++ member) vg::ChainIterator::operator!= (C++ function) vg::ChainIterator::operator* (C++ function) vg::ChainIterator::operator++ (C++ function) vg::ChainIterator::operator-> (C++ function) vg::ChainIterator::operator== (C++ function) vg::ChainIterator::pos (C++ member) vg::ChainIterator::scratch (C++ member) vg::char_to_string (C++ function) vg::choose_ln (C++ function) vg::cigar_against_path (C++ function) vg::cigar_string (C++ function) vg::cluster_cover (C++ function) vg::cluster_coverage (C++ function) vg::cluster_nodes (C++ function) vg::cluster_subgraph (C++ function), [1] vg::clusters_overlap_in_graph (C++ function) vg::clusters_overlap_in_read (C++ function) vg::clusters_overlap_length (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::COMPLEMENTARY_NUCLEOTIDES (C++ member) vg::compute_side_components (C++ function) vg::concat_mappings (C++ function) vg::concat_paths (C++ function) vg::Configurable (C++ class) vg::Configurable::get_name (C++ function) vg::Configurable::get_options (C++ function) vg::Configurable::option_offsets (C++ member) vg::Configurable::register_option (C++ function) vg::ConfigurableParser (C++ class) vg::ConfigurableParser::available_short_options (C++ member) vg::ConfigurableParser::codes_by_option (C++ member) vg::ConfigurableParser::ConfigurableParser (C++ function) vg::ConfigurableParser::configurables (C++ member) vg::ConfigurableParser::handle_base_option (C++ member) vg::ConfigurableParser::long_options (C++ member) vg::ConfigurableParser::long_options_used (C++ member) vg::ConfigurableParser::options_by_code (C++ member) vg::ConfigurableParser::parse (C++ function) vg::ConfigurableParser::print_help (C++ function) vg::ConfigurableParser::register_configurable (C++ function) vg::ConfigurableParser::short_options (C++ member) vg::connected_components (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::allowed_vcf_names (C++ member) vg::Constructor::allowed_vcf_regions (C++ member) vg::Constructor::alt_paths (C++ member) vg::Constructor::alts_as_loci (C++ member) vg::Constructor::bases_per_chunk (C++ member) vg::Constructor::chain_deletions (C++ member) vg::Constructor::condense_edits (C++ function) vg::Constructor::construct_chunk (C++ function) vg::Constructor::construct_graph (C++ function), [1] vg::Constructor::do_svs (C++ member) vg::Constructor::flat (C++ member) vg::Constructor::get_bounds (C++ function) vg::Constructor::greedy_pieces (C++ member) vg::Constructor::max_id (C++ member) vg::Constructor::max_node_size (C++ member) vg::Constructor::symbolic_allele_warnings (C++ member) vg::Constructor::trim_to_variable (C++ function) vg::Constructor::vars_per_chunk (C++ member) vg::Constructor::warn_on_lowercase (C++ member) vg::Constructor::warned_sequences (C++ member) vg::convert (C++ function), [1] 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::deconstruct (C++ function), [1] vg::Deconstructor::Deconstructor (C++ function) vg::Deconstructor::get_alleles (C++ function) vg::Deconstructor::headered (C++ member) vg::Deconstructor::pindexes (C++ member) vg::Deconstructor::~Deconstructor (C++ function) vg::default_full_length_bonus (C++ member) 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::DeleteHaplotypeCommand (C++ class) vg::DeleteHaplotypeCommand::deletions (C++ member) vg::DeleteHaplotypeCommand::execute (C++ function) vg::DeleteHaplotypeCommand::~DeleteHaplotypeCommand (C++ function) vg::DepthMap (C++ class) vg::DepthMap::DepthMap (C++ function), [1], [2] vg::DepthMap::depths (C++ member) vg::DepthMap::fill_depth (C++ function) vg::DepthMap::g_graph (C++ member) vg::DepthMap::get_depth (C++ function) vg::DepthMap::increment_depth (C++ function) vg::DepthMap::node_pos (C++ member) vg::DepthMap::set_depth (C++ function) vg::DepthMap::size (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::EdgeMapping (C++ type) 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_count (C++ function) 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::end_backward (C++ function) vg::entropy (C++ function), [1] vg::Exact (C++ class) vg::ExactMatchNode (C++ class) vg::ExactMatchNode::begin (C++ member) vg::ExactMatchNode::edges (C++ member) vg::ExactMatchNode::end (C++ member) vg::ExactMatchNode::path (C++ member) vg::ExhaustiveTraversalFinder (C++ class) vg::ExhaustiveTraversalFinder::add_traversals (C++ function) vg::ExhaustiveTraversalFinder::ExhaustiveTraversalFinder (C++ function) vg::ExhaustiveTraversalFinder::find_traversals (C++ function) vg::ExhaustiveTraversalFinder::graph (C++ member) vg::ExhaustiveTraversalFinder::include_reversing_traversals (C++ member) vg::ExhaustiveTraversalFinder::snarl_manager (C++ member) vg::ExhaustiveTraversalFinder::stack_up_valid_walks (C++ function) vg::ExhaustiveTraversalFinder::~ExhaustiveTraversalFinder (C++ function) vg::extend_alignment (C++ function) vg::extend_path (C++ function) vg::extract_sub_multipath_alignment (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_interleaved_for_each_parallel_after_wait (C++ function) vg::fastq_paired_two_files_for_each (C++ function) vg::fastq_paired_two_files_for_each_parallel (C++ function) vg::fastq_paired_two_files_for_each_parallel_after_wait (C++ function) vg::fastq_unpaired_for_each (C++ function) vg::fastq_unpaired_for_each_parallel (C++ function) vg::FeatureSet (C++ class) vg::FeatureSet::Feature (C++ class) vg::FeatureSet::Feature::extra_data (C++ member) vg::FeatureSet::Feature::feature_name (C++ member) vg::FeatureSet::Feature::first (C++ member) vg::FeatureSet::Feature::last (C++ member) vg::FeatureSet::Feature::path_name (C++ member) vg::FeatureSet::features (C++ member) vg::FeatureSet::get_features (C++ function) vg::FeatureSet::load_bed (C++ function) vg::FeatureSet::on_path_edit (C++ function) vg::FeatureSet::save_bed (C++ function) vg::Filter (C++ class) vg::Filter::anchored_filter (C++ function) vg::Filter::avg_qual_filter (C++ function) vg::Filter::breakend_filter (C++ function) vg::Filter::coverage_filter (C++ function) vg::Filter::deletion_filter (C++ function) vg::Filter::depth_filter (C++ function) vg::Filter::distance_between_positions (C++ function) vg::Filter::do_remap (C++ member) vg::Filter::duplication_filter (C++ function) vg::Filter::fill_node_to_position (C++ function) vg::Filter::Filter (C++ function) vg::Filter::filter_matches (C++ member) vg::Filter::gcsa_ind (C++ member) vg::Filter::get_clipped_position (C++ function) vg::Filter::get_clipped_ref_position (C++ function) vg::Filter::get_clipped_seq (C++ function) vg::Filter::init_mapper (C++ function) vg::Filter::insert_mean (C++ member) vg::Filter::insert_sd (C++ member) vg::Filter::insert_size_filter (C++ function) vg::Filter::insertion_filter (C++ function) vg::Filter::interchromosomal_filter (C++ function) vg::Filter::inverse (C++ member) vg::Filter::inversion_filter (C++ function) vg::Filter::is_left_clipped (C++ function) vg::Filter::lcp_ind (C++ member) vg::Filter::mark_smallVariant_alignments (C++ function) vg::Filter::mark_sv_alignments (C++ function) vg::Filter::max_path_length (C++ member) 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_mapper (C++ member) vg::Filter::my_max_distance (C++ member) vg::Filter::my_vg (C++ member) vg::Filter::my_xg_index (C++ member) vg::Filter::node_to_position (C++ member) vg::Filter::one_end_anchored_filter (C++ function) vg::Filter::pair_orientation_filter (C++ function) vg::Filter::path_divergence_filter (C++ function) vg::Filter::path_length_filter (C++ function) vg::Filter::percent_identity_filter (C++ function) vg::Filter::perfect_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::refactor_split_alignment (C++ function) vg::Filter::remap (C++ function), [1] vg::Filter::remove_clipped_portion (C++ function) vg::Filter::remove_failing_edits (C++ member) vg::Filter::reversing_filter (C++ function) vg::Filter::set_avg (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_remove_failing_edits (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::unmapped_filter (C++ function) vg::Filter::use_avg (C++ member) vg::Filter::window_length (C++ member) vg::Filter::~Filter (C++ function) vg::final_position (C++ function) vg::find_temp_dir (C++ function) vg::first_path_position (C++ function) vg::fit_zipf (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_doubly_reversed_edges (C++ function) vg::flip_nodes (C++ function) vg::FlowSort (C++ class) vg::FlowSort::bfs (C++ function) vg::FlowSort::DEFAULT_PATH_WEIGHT (C++ member) vg::FlowSort::dfs (C++ function) vg::FlowSort::erase_in_out_edges (C++ function) vg::FlowSort::fast_linear_sort (C++ function) vg::FlowSort::find_in_out_web (C++ function) vg::FlowSort::find_max_node (C++ function) vg::FlowSort::flow_sort_nodes (C++ function) vg::FlowSort::FlowSort (C++ function) vg::FlowSort::from_simple_reverse (C++ function) vg::FlowSort::from_simple_reverse_orientation (C++ function) vg::FlowSort::get_cc_in_wg (C++ function) vg::FlowSort::get_next_node_recalc_degrees (C++ function) vg::FlowSort::get_node_degree (C++ function) vg::FlowSort::groom_components (C++ function) vg::FlowSort::Growth (C++ class) vg::FlowSort::Growth::backbone (C++ member) vg::FlowSort::Growth::Growth (C++ function) vg::FlowSort::Growth::nodes (C++ member) vg::FlowSort::Growth::ref_path (C++ member) vg::FlowSort::mark_dfs (C++ function) vg::FlowSort::max_flow_sort (C++ function) vg::FlowSort::min_cut (C++ function) vg::FlowSort::process_in_out_growth (C++ function) vg::FlowSort::remove_edge (C++ function) vg::FlowSort::reverse_edge (C++ function) vg::FlowSort::reverse_from_start_to_end_edge (C++ function) vg::FlowSort::to_simple_reverse (C++ function) vg::FlowSort::to_simple_reverse_orientation (C++ function) vg::FlowSort::update_in_out_edges (C++ function) vg::FlowSort::vg (C++ member) vg::FlowSort::WeightedGraph (C++ class) vg::FlowSort::WeightedGraph::construct (C++ function) vg::FlowSort::WeightedGraph::edge_weight (C++ member) vg::FlowSort::WeightedGraph::edges_in_nodes (C++ member) vg::FlowSort::WeightedGraph::edges_out_nodes (C++ member) vg::FragmentLengthDistribution (C++ class) vg::FragmentLengthDistribution::curr_sample_size (C++ function) vg::FragmentLengthDistribution::estimate_distribution (C++ function) vg::FragmentLengthDistribution::force_parameters (C++ function) vg::FragmentLengthDistribution::FragmentLengthDistribution (C++ function), [1] vg::FragmentLengthDistribution::is_finalized (C++ function) vg::FragmentLengthDistribution::is_fixed (C++ member) vg::FragmentLengthDistribution::lengths (C++ member) vg::FragmentLengthDistribution::max_sample_size (C++ function) vg::FragmentLengthDistribution::maximum_sample_size (C++ member) vg::FragmentLengthDistribution::mean (C++ function) vg::FragmentLengthDistribution::measurements_begin (C++ function) vg::FragmentLengthDistribution::measurements_end (C++ function) vg::FragmentLengthDistribution::mu (C++ member) vg::FragmentLengthDistribution::reestimation_frequency (C++ member) vg::FragmentLengthDistribution::register_fragment_length (C++ function) vg::FragmentLengthDistribution::robust_estimation_fraction (C++ member) vg::FragmentLengthDistribution::sigma (C++ member) vg::FragmentLengthDistribution::stdev (C++ function) vg::FragmentLengthDistribution::~FragmentLengthDistribution (C++ function) vg::FragmentLengthStatistics (C++ class) vg::FragmentLengthStatistics::cached_fragment_direction (C++ member) vg::FragmentLengthStatistics::cached_fragment_length_mean (C++ member) vg::FragmentLengthStatistics::cached_fragment_length_stdev (C++ member) vg::FragmentLengthStatistics::cached_fragment_orientation_same (C++ member) vg::FragmentLengthStatistics::fixed_fragment_model (C++ member) vg::FragmentLengthStatistics::fragment_direction (C++ function) vg::FragmentLengthStatistics::fragment_directions (C++ member) vg::FragmentLengthStatistics::fragment_length_cache_size (C++ member) vg::FragmentLengthStatistics::fragment_length_mean (C++ function) vg::FragmentLengthStatistics::fragment_length_pdf (C++ function) vg::FragmentLengthStatistics::fragment_length_pval (C++ function) vg::FragmentLengthStatistics::fragment_length_stdev (C++ function) vg::FragmentLengthStatistics::fragment_lengths (C++ member) vg::FragmentLengthStatistics::fragment_max (C++ member) vg::FragmentLengthStatistics::fragment_model_str (C++ function) vg::FragmentLengthStatistics::fragment_model_update_interval (C++ member) vg::FragmentLengthStatistics::fragment_orientation (C++ function) vg::FragmentLengthStatistics::fragment_orientations (C++ member) vg::FragmentLengthStatistics::fragment_sigma (C++ member) vg::FragmentLengthStatistics::fragment_size (C++ member) vg::FragmentLengthStatistics::perfect_pair_identity_threshold (C++ member) vg::FragmentLengthStatistics::record_fragment_configuration (C++ function) vg::FragmentLengthStatistics::save_frag_lens_to_alns (C++ function) vg::FragmentLengthStatistics::since_last_fragment_length_estimate (C++ member) vg::from_length (C++ function) vg::from_length_after_pos (C++ function) vg::from_length_before_pos (C++ function) vg::gamma_ln (C++ function) vg::GAMSorter (C++ class) vg::GAMSorter::max_buf_size (C++ member) vg::GAMSorter::paired_pairs (C++ member) vg::GAMSorter::pairs (C++ member) vg::GAMSorter::split_to_split_size (C++ member) vg::GAMSorter::tmp_filenames (C++ member) vg::GAMSorter::tmp_files (C++ member) vg::gcsa_nodes_to_positions (C++ function) vg::GenomeState (C++ class) vg::GenomeState::append_haplotype (C++ function) vg::GenomeState::backing_graph (C++ member) vg::GenomeState::count_haplotypes (C++ function), [1] vg::GenomeState::delete_haplotype (C++ function) vg::GenomeState::dump (C++ function) vg::GenomeState::execute (C++ function) vg::GenomeState::GenomeState (C++ function) vg::GenomeState::get_net_graph (C++ function) vg::GenomeState::insert_handles (C++ function) vg::GenomeState::insert_haplotype (C++ function) vg::GenomeState::manager (C++ member) vg::GenomeState::net_graphs (C++ member) vg::GenomeState::replace_local_haplotype (C++ function) vg::GenomeState::replace_snarl_haplotype (C++ function) vg::GenomeState::state (C++ member) vg::GenomeState::swap_haplotypes (C++ function) vg::GenomeState::telomeres (C++ member) vg::GenomeState::trace_haplotype (C++ function) vg::GenomeStateCommand (C++ class) vg::GenomeStateCommand::execute (C++ function) vg::GenomeStateCommand::~GenomeStateCommand (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::genotype_svs (C++ function) 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_snarls (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::deleted_prior_logprob (C++ member) vg::Genotyper::diploid_prior_logprob (C++ member) vg::Genotyper::edge_allele_labels (C++ function) vg::Genotyper::genotype_snarl (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_snarl (C++ function) vg::Genotyper::get_qualities_in_snarl (C++ function) vg::Genotyper::get_snarl_reference_bounds (C++ function) vg::Genotyper::get_traversal_of_snarl (C++ function) vg::Genotyper::haploid_prior_logprob (C++ member) 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::mapping_enters_side (C++ function) vg::Genotyper::mapping_exits_side (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::polyploid_prior_success_logprob (C++ member) vg::Genotyper::print_statistics (C++ function) vg::Genotyper::quality_aligner (C++ member) vg::Genotyper::realign_indels (C++ member) vg::Genotyper::report_snarl (C++ function) vg::Genotyper::report_snarl_traversal (C++ function) vg::Genotyper::run (C++ function) vg::Genotyper::snarl_reference_length_histogram (C++ member) vg::Genotyper::snarl_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::geometric_sampling_prob_ln (C++ function) vg::get_end_of (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_output_file_name (C++ function) vg::get_pileup_line (C++ function) vg::get_start_of (C++ function) vg::get_thread_count (C++ function) vg::get_traversal_support (C++ function) vg::getReachableBridges (C++ function) vg::getReachableBridges2 (C++ function) vg::Graph (C++ class) vg::Graph::edge (C++ member) vg::Graph::node (C++ member) vg::Graph::path (C++ member) vg::GraphSynchronizer (C++ class) vg::GraphSynchronizer::get_path_index (C++ function) vg::GraphSynchronizer::get_path_sequence (C++ function) vg::GraphSynchronizer::graph (C++ member) vg::GraphSynchronizer::GraphSynchronizer (C++ function) vg::GraphSynchronizer::indexes (C++ member) vg::GraphSynchronizer::Lock (C++ class) vg::GraphSynchronizer::Lock::apply_edit (C++ function), [1] vg::GraphSynchronizer::Lock::apply_full_length_edit (C++ function) vg::GraphSynchronizer::Lock::context_bases (C++ member) vg::GraphSynchronizer::Lock::endpoints (C++ member) vg::GraphSynchronizer::Lock::get_endpoints (C++ function) vg::GraphSynchronizer::Lock::get_peripheral_attachments (C++ function) vg::GraphSynchronizer::Lock::get_subgraph (C++ function) vg::GraphSynchronizer::Lock::Lock (C++ function), [1] vg::GraphSynchronizer::Lock::lock (C++ function) vg::GraphSynchronizer::Lock::locked_nodes (C++ member) vg::GraphSynchronizer::Lock::past_end (C++ member) vg::GraphSynchronizer::Lock::path_name (C++ member) vg::GraphSynchronizer::Lock::path_offset (C++ member) vg::GraphSynchronizer::Lock::peripheral_attachments (C++ member) vg::GraphSynchronizer::Lock::periphery (C++ member) vg::GraphSynchronizer::Lock::reflect (C++ member) vg::GraphSynchronizer::Lock::start (C++ member) vg::GraphSynchronizer::Lock::subgraph (C++ member) vg::GraphSynchronizer::Lock::synchronizer (C++ member) vg::GraphSynchronizer::Lock::unlock (C++ function) vg::GraphSynchronizer::locked_nodes (C++ member) vg::GraphSynchronizer::update_path_indexes (C++ function) vg::GraphSynchronizer::wait_for_region (C++ member) vg::GraphSynchronizer::whole_graph_lock (C++ member) vg::GraphSynchronizer::with_path_index (C++ function) vg::handle_t (C++ class) vg::handle_t::data (C++ member) vg::HandleGraph (C++ class) vg::HandleGraph::edge_handle (C++ function) vg::HandleGraph::flip (C++ function) vg::HandleGraph::follow_edges (C++ function), [1] vg::HandleGraph::for_each_handle (C++ function), [1] vg::HandleGraph::forward (C++ function) vg::HandleGraph::get_handle (C++ function), [1] vg::HandleGraph::get_id (C++ function) vg::HandleGraph::get_is_reverse (C++ function) vg::HandleGraph::get_length (C++ function) vg::HandleGraph::get_sequence (C++ function) vg::HandleGraph::node_size (C++ function) vg::HandleGraph::to_visit (C++ function) vg::has_inversion (C++ function) 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::Homogenizer (C++ class) vg::Homogenizer::remap (C++ function) vg::Homogenizer::translator (C++ member) 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::identify_start_subpaths (C++ function) vg::identity (C++ function) vg::increment_node_mapping_ids (C++ function) vg::IncrementIter (C++ class) vg::IncrementIter::current (C++ member) vg::IncrementIter::IncrementIter (C++ function) vg::IncrementIter::operator!= (C++ function) vg::IncrementIter::operator* (C++ function) vg::IncrementIter::operator++ (C++ function), [1] vg::IncrementIter::operator= (C++ function) vg::IncrementIter::operator== (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::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_of (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::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::metadata_entry_to_string (C++ function) vg::Index::name (C++ member) vg::Index::new_path_id (C++ function) vg::Index::next_nonce (C++ member) 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::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::threads (C++ member) vg::Index::traversal_entry_to_string (C++ function) 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::initial_position (C++ function) vg::InsertHaplotypeCommand (C++ class) vg::InsertHaplotypeCommand::execute (C++ function) vg::InsertHaplotypeCommand::insertions (C++ member) vg::InsertHaplotypeCommand::~InsertHaplotypeCommand (C++ function) vg::integer_power (C++ function), [1] vg::IntervalBitfield (C++ class) vg::IntervalBitfield::add (C++ function) vg::IntervalBitfield::collides (C++ function) vg::IntervalBitfield::IntervalBitfield (C++ function) vg::IntervalBitfield::used (C++ member) vg::is_all_n (C++ function) vg::is_empty (C++ function) vg::is_id_sortable (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::ln_to_log10 (C++ function) vg::LocationSupport (C++ class) vg::LocationSupport::node_id (C++ member) vg::LocationSupport::oneof_location (C++ member) vg::LocationSupport::support (C++ member) vg::Locus (C++ class) vg::Locus::allele (C++ member) vg::Locus::allele_log_likelihood (C++ member) vg::Locus::genotype (C++ member) vg::Locus::name (C++ member) vg::Locus::overall_support (C++ member) vg::Locus::support (C++ member) vg::log10_to_ln (C++ function) vg::LOG_ZERO (C++ member) vg::logprob_add (C++ function) vg::logprob_geometric_mean (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], [2] vg::make_position (C++ function), [1], [2] vg::make_support (C++ function) vg::make_variant_id (C++ function) vg::map_keys_to_set (C++ function) vg::map_over (C++ function) vg::Mapper (C++ class) vg::Mapper::adjacent_positions (C++ function) vg::Mapper::align (C++ function), [1] vg::Mapper::align_banded (C++ function) vg::Mapper::align_cluster (C++ function) vg::Mapper::align_maybe_flip (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_paired_multi (C++ function) vg::Mapper::align_to_graph (C++ function) vg::Mapper::alignment_end_position (C++ function) vg::Mapper::alignment_initial_path_positions (C++ function) vg::Mapper::alignment_path_offsets (C++ function) vg::Mapper::alignment_refpos_to_path_offsets (C++ function) vg::Mapper::alignment_subgraph (C++ function) vg::Mapper::alignments_consistent (C++ function) vg::Mapper::always_rescue (C++ member) vg::Mapper::annotate_with_initial_path_positions (C++ function), [1] vg::Mapper::approx_alignment_position (C++ function) vg::Mapper::approx_distance (C++ function) vg::Mapper::approx_fragment_length (C++ function) vg::Mapper::approx_position (C++ function) vg::Mapper::average_node_length (C++ function) vg::Mapper::band_multimaps (C++ member) vg::Mapper::check_alignment (C++ function) vg::Mapper::cluster_subgraph_strict (C++ function) vg::Mapper::clusters_to_drop (C++ function) vg::Mapper::compute_cluster_mapping_quality (C++ function) vg::Mapper::compute_mapping_qualities (C++ function), [1] vg::Mapper::compute_uniqueness (C++ function) vg::Mapper::context_depth (C++ member) vg::Mapper::debug (C++ member) vg::Mapper::drop_chain (C++ member) vg::Mapper::estimate_max_possible_mapping_quality (C++ function) vg::Mapper::extra_multimaps (C++ member) vg::Mapper::filter_and_process_multimaps (C++ function) vg::Mapper::frag_stats (C++ member) vg::Mapper::get_node_length (C++ function) vg::Mapper::graph_distance (C++ function) vg::Mapper::graph_entropy (C++ function) vg::Mapper::graph_mixed_distance_estimate (C++ function) vg::Mapper::identity_weight (C++ member) vg::Mapper::imperfect_pairs_to_retry (C++ member) vg::Mapper::include_full_length_bonuses (C++ member) vg::Mapper::likely_mate_position (C++ function) vg::Mapper::likely_mate_positions (C++ function) vg::Mapper::make_bands (C++ function) vg::Mapper::Mapper (C++ function), [1] vg::Mapper::mate_rescues (C++ member) vg::Mapper::max_attempts (C++ member) vg::Mapper::max_band_jump (C++ member) vg::Mapper::max_cluster_mapping_quality (C++ member) vg::Mapper::max_multimaps (C++ member) vg::Mapper::max_possible_mapping_quality (C++ function) vg::Mapper::max_query_graph_ratio (C++ member) vg::Mapper::max_softclip_iterations (C++ member) vg::Mapper::max_target_factor (C++ member) vg::Mapper::maybe_mq_threshold (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_to_alignment (C++ function) vg::Mapper::min_banded_mq (C++ member) vg::Mapper::min_cluster_length (C++ member) vg::Mapper::min_identity (C++ member) vg::Mapper::min_multimaps (C++ member) vg::Mapper::min_pair_fragment_length (C++ function) vg::Mapper::mq_overlap (C++ member) vg::Mapper::node_approximately_at (C++ function) vg::Mapper::node_positions_in_paths (C++ function) vg::Mapper::pair_consistent (C++ function) vg::Mapper::pair_rescue (C++ function) vg::Mapper::pair_rescue_hang_threshold (C++ member) vg::Mapper::pair_rescue_retry_threshold (C++ member) vg::Mapper::patch_alignment (C++ function) vg::Mapper::realign_from_start_position (C++ function) vg::Mapper::remove_full_length_bonuses (C++ function) vg::Mapper::resolve_paired_mems (C++ function) vg::Mapper::score_alignment (C++ function) vg::Mapper::score_sort_and_deduplicate_alignments (C++ function) vg::Mapper::simultaneous_pair_alignment (C++ member) vg::Mapper::softclip_threshold (C++ member) vg::Mapper::surject_alignment (C++ function) vg::Mapper::thread_extension (C++ member) vg::Mapper::use_cluster_mq (C++ member) vg::Mapper::walk_match (C++ function), [1] 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_perfect_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::MAX_ALLELE_LENGTH (C++ member) vg::MaximalExactMatch (C++ class) vg::MaximalExactMatch::begin (C++ member) vg::MaximalExactMatch::count_Ns (C++ function) vg::MaximalExactMatch::end (C++ member) vg::MaximalExactMatch::fragment (C++ member) vg::MaximalExactMatch::length (C++ function) vg::MaximalExactMatch::match_count (C++ member) vg::MaximalExactMatch::MaximalExactMatch (C++ function), [1], [2], [3] vg::MaximalExactMatch::nodes (C++ member) vg::MaximalExactMatch::operator= (C++ function), [1] vg::MaximalExactMatch::positions (C++ member) vg::MaximalExactMatch::primary (C++ member) vg::MaximalExactMatch::range (C++ member) vg::MaximalExactMatch::sequence (C++ function) vg::maxSup (C++ function) vg::median (C++ function) vg::mem_min_oriented_distances (C++ function) vg::MEMChainModel (C++ class) vg::MEMChainModel::clear_scores (C++ function) vg::MEMChainModel::display (C++ function) vg::MEMChainModel::max_vertex (C++ function) vg::MEMChainModel::MEMChainModel (C++ function) vg::MEMChainModel::model (C++ member) vg::MEMChainModel::positions (C++ member) vg::MEMChainModel::redundant_vertexes (C++ member) vg::MEMChainModel::score (C++ function) vg::MEMChainModel::traceback (C++ function) vg::MEMChainModelVertex (C++ class) vg::MEMChainModelVertex::mem (C++ member) vg::MEMChainModelVertex::MEMChainModelVertex (C++ function), [1], [2] vg::MEMChainModelVertex::next_cost (C++ member) vg::MEMChainModelVertex::operator= (C++ function), [1] vg::MEMChainModelVertex::prev (C++ member) vg::MEMChainModelVertex::prev_cost (C++ member) vg::MEMChainModelVertex::score (C++ member) vg::MEMChainModelVertex::weight (C++ member) vg::MEMChainModelVertex::~MEMChainModelVertex (C++ function) vg::mems_overlap (C++ function) vg::mems_overlap_length (C++ function) vg::mems_to_json (C++ function) vg::merge_adjacent_edits (C++ function), [1] vg::merge_alignments (C++ function), [1] vg::mergeNodeObjects (C++ function) vg::middle_signature (C++ function), [1] vg::min_oriented_distances (C++ function) vg::minSup (C++ function) vg::modular_exponent (C++ function) vg::multinomial_censored_sampling_prob_ln (C++ function) vg::multinomial_choose_ln (C++ function) vg::multinomial_sampling_prob_ln (C++ function) vg::MultipathAlignment (C++ class) vg::MultipathAlignment::mapping_quality (C++ member) vg::MultipathAlignment::name (C++ member) vg::MultipathAlignment::paired_read_name (C++ member) vg::MultipathAlignment::quality (C++ member) vg::MultipathAlignment::read_group (C++ member) vg::MultipathAlignment::sample_name (C++ member) vg::MultipathAlignment::sequence (C++ member) vg::MultipathAlignment::start (C++ member) vg::MultipathAlignment::subpath (C++ member) vg::MultipathAlignmentGraph (C++ class) vg::MultipathAlignmentGraph::match_nodes (C++ member) vg::MultipathAlignmentGraph::MultipathAlignmentGraph (C++ function) vg::MultipathAlignmentGraph::prune_to_high_scoring_paths (C++ function) vg::MultipathAlignmentGraph::remove_transitive_edges (C++ function) vg::MultipathAlignmentGraph::reorder_adjacency_lists (C++ function) vg::MultipathAlignmentGraph::topological_sort (C++ function) vg::MultipathAlignmentGraph::~MultipathAlignmentGraph (C++ function) vg::MultipathMapper (C++ class) vg::MultipathMapper::align_to_cluster_graph_pairs (C++ function) vg::MultipathMapper::align_to_cluster_graphs (C++ function) vg::MultipathMapper::align_to_cluster_graphs_with_rescue (C++ function) vg::MultipathMapper::are_consistent (C++ function) vg::MultipathMapper::attempt_rescue (C++ function) vg::MultipathMapper::attempt_unpaired_multipath_map_of_pair (C++ function) vg::MultipathMapper::band_padding (C++ member) vg::MultipathMapper::clustergraph_t (C++ type) vg::MultipathMapper::distance_between (C++ function) vg::MultipathMapper::fragment_length_log_likelihood (C++ function) vg::MultipathMapper::is_consistent (C++ function) vg::MultipathMapper::likely_mismapping (C++ function) vg::MultipathMapper::log_likelihood_approx_factor (C++ member) vg::MultipathMapper::max_expected_dist_approx_error (C++ member) vg::MultipathMapper::max_p_value_memo_size (C++ member) vg::MultipathMapper::max_snarl_cut_size (C++ member) vg::MultipathMapper::max_suboptimal_path_score_ratio (C++ member) vg::MultipathMapper::mem_coverage_min_ratio (C++ member) vg::MultipathMapper::memcluster_t (C++ type) vg::MultipathMapper::min_clustering_mem_length (C++ member) vg::MultipathMapper::multipath_align (C++ function) vg::MultipathMapper::multipath_map (C++ function) vg::MultipathMapper::multipath_map_internal (C++ function) vg::MultipathMapper::multipath_map_paired (C++ function) vg::MultipathMapper::MultipathMapper (C++ function) vg::MultipathMapper::num_alt_alns (C++ member) vg::MultipathMapper::num_mapping_attempts (C++ member) vg::MultipathMapper::p_value_memo (C++ member) vg::MultipathMapper::query_cluster_graphs (C++ function) vg::MultipathMapper::random_match_p_value (C++ function) vg::MultipathMapper::read_coverage (C++ function) vg::MultipathMapper::read_coverage_z_score (C++ function) vg::MultipathMapper::score_pseudo_length (C++ function) vg::MultipathMapper::set_automatic_min_clustering_length (C++ function) vg::MultipathMapper::share_start_position (C++ function) vg::MultipathMapper::snarl_manager (C++ member) vg::MultipathMapper::sort_and_compute_mapping_quality (C++ function), [1] vg::MultipathMapper::split_multicomponent_alignments (C++ function), [1] vg::MultipathMapper::strip_full_length_bonuses (C++ function) vg::MultipathMapper::validate_multipath_alignment (C++ function) vg::MultipathMapper::~MultipathMapper (C++ function) vg::MutableHandleGraph (C++ class) vg::MutableHandleGraph::apply_orientation (C++ function) vg::MutableHandleGraph::create_edge (C++ function) vg::MutableHandleGraph::create_handle (C++ function) vg::MutableHandleGraph::destroy_edge (C++ function) vg::MutableHandleGraph::destroy_handle (C++ function) vg::MutableHandleGraph::divide_handle (C++ function), [1] vg::MutableHandleGraph::swap_handles (C++ function) vg::NameMapper (C++ class) vg::NameMapper::add_name_mapping (C++ function) vg::NameMapper::fasta_to_vcf (C++ function) vg::NameMapper::fasta_to_vcf_renames (C++ member) vg::NameMapper::vcf_to_fasta (C++ function) vg::NameMapper::vcf_to_fasta_renames (C++ member) vg::NestedTraversalFinder (C++ class) vg::NestedTraversalFinder::augmented (C++ member) vg::NestedTraversalFinder::bp_length (C++ function) vg::NestedTraversalFinder::find_bubble (C++ function) vg::NestedTraversalFinder::find_traversals (C++ function) vg::NestedTraversalFinder::min_support_in_path (C++ function) vg::NestedTraversalFinder::NestedTraversalFinder (C++ function) vg::NestedTraversalFinder::search_left (C++ function) vg::NestedTraversalFinder::search_right (C++ function) vg::NestedTraversalFinder::snarl_manager (C++ member) vg::NestedTraversalFinder::verbose (C++ member) vg::NestedTraversalFinder::~NestedTraversalFinder (C++ function) vg::NetGraph (C++ class) vg::NetGraph::add_chain_child (C++ function) vg::NetGraph::add_unary_child (C++ function) vg::NetGraph::chain_end_rewrites (C++ member) vg::NetGraph::chain_ends_by_start (C++ member) vg::NetGraph::connectivity (C++ member) vg::NetGraph::end (C++ member) vg::NetGraph::flip (C++ function) vg::NetGraph::follow_edges (C++ function) vg::NetGraph::for_each_handle (C++ function) vg::NetGraph::get_end (C++ function) vg::NetGraph::get_handle (C++ function) vg::NetGraph::get_id (C++ function) vg::NetGraph::get_inward_backing_handle (C++ function) vg::NetGraph::get_is_reverse (C++ function) vg::NetGraph::get_length (C++ function) vg::NetGraph::get_sequence (C++ function) vg::NetGraph::get_start (C++ function) vg::NetGraph::graph (C++ member) vg::NetGraph::is_child (C++ function) vg::NetGraph::NetGraph (C++ function), [1], [2], [3] vg::NetGraph::node_size (C++ function) vg::NetGraph::start (C++ member) vg::NetGraph::unary_boundaries (C++ member) vg::NetGraph::use_internal_connectivity (C++ member) vg::NGSSimulator (C++ class) vg::NGSSimulator::advance (C++ function) vg::NGSSimulator::advance_by_distance (C++ function) vg::NGSSimulator::advance_on_graph (C++ function) vg::NGSSimulator::advance_on_graph_by_distance (C++ function) vg::NGSSimulator::advance_on_path (C++ function) vg::NGSSimulator::advance_on_path_by_distance (C++ function) vg::NGSSimulator::alphabet (C++ member) vg::NGSSimulator::apply_aligned_base (C++ function) vg::NGSSimulator::apply_deletion (C++ function) vg::NGSSimulator::apply_insertion (C++ function) vg::NGSSimulator::background_sampler (C++ member) vg::NGSSimulator::edge_cache (C++ member) vg::NGSSimulator::finalize (C++ function) vg::NGSSimulator::get_read_name (C++ function) vg::NGSSimulator::indel_error_prop (C++ member) vg::NGSSimulator::indel_poly_rate (C++ member) vg::NGSSimulator::insert_mean (C++ member) vg::NGSSimulator::insert_sampler (C++ member) vg::NGSSimulator::insert_sd (C++ member) vg::NGSSimulator::joint_initial_distr (C++ member) vg::NGSSimulator::MarkovDistribution (C++ class) vg::NGSSimulator::MarkovDistribution::column_of (C++ member) vg::NGSSimulator::MarkovDistribution::cond_distrs (C++ member) vg::NGSSimulator::MarkovDistribution::finalize (C++ function) vg::NGSSimulator::MarkovDistribution::MarkovDistribution (C++ function) vg::NGSSimulator::MarkovDistribution::prng (C++ member) vg::NGSSimulator::MarkovDistribution::record_transition (C++ function) vg::NGSSimulator::MarkovDistribution::sample_transition (C++ function) vg::NGSSimulator::MarkovDistribution::samplers (C++ member) vg::NGSSimulator::MarkovDistribution::value_at (C++ member) vg::NGSSimulator::mut_sampler (C++ member) vg::NGSSimulator::mutation_alphabets (C++ member) vg::NGSSimulator::NGSSimulator (C++ function), [1] vg::NGSSimulator::node_cache (C++ member) vg::NGSSimulator::path_sampler (C++ member) vg::NGSSimulator::phred_prob (C++ member) vg::NGSSimulator::prng (C++ member) vg::NGSSimulator::prob_sampler (C++ member) vg::NGSSimulator::record_read_pair_quality (C++ function) vg::NGSSimulator::record_read_quality (C++ function) vg::NGSSimulator::retry_on_Ns (C++ member) vg::NGSSimulator::sample_counter (C++ member) vg::NGSSimulator::sample_read (C++ function) vg::NGSSimulator::sample_read_internal (C++ function) vg::NGSSimulator::sample_read_pair (C++ function) vg::NGSSimulator::sample_read_quality (C++ function) vg::NGSSimulator::sample_read_quality_internal (C++ function) vg::NGSSimulator::sample_read_quality_pair (C++ function) vg::NGSSimulator::sample_start_graph_pos (C++ function) vg::NGSSimulator::sample_start_path_pos (C++ function) vg::NGSSimulator::sample_start_pos (C++ function) vg::NGSSimulator::seed (C++ member) vg::NGSSimulator::source_paths (C++ member) vg::NGSSimulator::start_pos_samplers (C++ member) vg::NGSSimulator::strand_sampler (C++ member) vg::NGSSimulator::sub_poly_rate (C++ member) vg::NGSSimulator::transition_distrs_1 (C++ member) vg::NGSSimulator::transition_distrs_2 (C++ member) vg::NGSSimulator::walk_backwards (C++ function) vg::NGSSimulator::xg_index (C++ member) vg::NoAlignmentInBandException (C++ class) 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::NodeSide::to_visit (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::normal_inverse_cdf (C++ function) vg::normal_pdf (C++ function) vg::off_t (C++ type) vg::offset (C++ function) vg::operator!= (C++ function), [1], [2], [3] vg::operator* (C++ function), [1] vg::operator*= (C++ function) vg::operator+ (C++ function) vg::operator+= (C++ function) vg::operator/ (C++ function) vg::operator/= (C++ function) vg::operator< (C++ function), [1], [2], [3], [4] vg::operator<< (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] vg::operator== (C++ function), [1], [2], [3], [4], [5] vg::operator> (C++ function) vg::optimal_alignment (C++ function) vg::optimal_alignment_internal (C++ function) vg::optimal_alignment_score (C++ function) vg::Option (C++ class) vg::Option::at (C++ function), [1] vg::Option::begin (C++ function), [1] vg::Option::empty (C++ function) vg::Option::end (C++ function), [1] vg::Option::Option (C++ function), [1] vg::Option::size (C++ function) vg::Option::~Option (C++ function), [1] vg::Option<vector<Item>, Parser> (C++ class) vg::Option<vector<Item>, Parser>::Value (C++ type) vg::OptionInterface (C++ class) vg::OptionInterface::get_default_value (C++ function) vg::OptionInterface::get_description (C++ function) vg::OptionInterface::get_long_option (C++ function) vg::OptionInterface::get_short_options (C++ function) vg::OptionInterface::has_argument (C++ function) vg::OptionInterface::parse (C++ function), [1] vg::OptionInterface::~OptionInterface (C++ function) vg::OptionValueParser (C++ class) vg::OptionValueParser::has_argument (C++ function), [1], [2] vg::OptionValueParser::parse (C++ function), [1], [2] vg::OptionValueParser::parse_default (C++ function), [1], [2] vg::OptionValueParser::unparse (C++ function), [1], [2] vg::OptionValueParser<vector<Item>> (C++ class) vg::OrientedDistanceClusterer (C++ class) vg::OrientedDistanceClusterer::aligner (C++ member) vg::OrientedDistanceClusterer::cluster_t (C++ type) vg::OrientedDistanceClusterer::clusters (C++ function) vg::OrientedDistanceClusterer::compute_tail_mem_coverage (C++ function) vg::OrientedDistanceClusterer::connected_components (C++ function) vg::OrientedDistanceClusterer::DPScoreComparator (C++ class) vg::OrientedDistanceClusterer::DPScoreComparator::DPScoreComparator (C++ function), [1] vg::OrientedDistanceClusterer::DPScoreComparator::nodes (C++ member) vg::OrientedDistanceClusterer::DPScoreComparator::operator() (C++ function) vg::OrientedDistanceClusterer::DPScoreComparator::~DPScoreComparator (C++ function) vg::OrientedDistanceClusterer::extend_dist_tree_by_path_buckets (C++ function) vg::OrientedDistanceClusterer::extend_dist_tree_by_permutations (C++ function) vg::OrientedDistanceClusterer::flatten_distance_tree (C++ function) vg::OrientedDistanceClusterer::get_on_strand_distance_tree (C++ function) vg::OrientedDistanceClusterer::handle_memo_t (C++ type) vg::OrientedDistanceClusterer::hit_t (C++ type) vg::OrientedDistanceClusterer::identify_sources_and_sinks (C++ function) vg::OrientedDistanceClusterer::node_occurrence_on_paths_memo_t (C++ type) vg::OrientedDistanceClusterer::nodes (C++ member) vg::OrientedDistanceClusterer::ODEdge (C++ class) vg::OrientedDistanceClusterer::ODEdge::ODEdge (C++ function), [1] vg::OrientedDistanceClusterer::ODEdge::to_idx (C++ member) vg::OrientedDistanceClusterer::ODEdge::weight (C++ member) vg::OrientedDistanceClusterer::ODEdge::~ODEdge (C++ function) vg::OrientedDistanceClusterer::ODNode (C++ class) vg::OrientedDistanceClusterer::ODNode::dp_score (C++ member) vg::OrientedDistanceClusterer::ODNode::edges_from (C++ member) vg::OrientedDistanceClusterer::ODNode::edges_to (C++ member) vg::OrientedDistanceClusterer::ODNode::mem (C++ member) vg::OrientedDistanceClusterer::ODNode::ODNode (C++ function), [1] vg::OrientedDistanceClusterer::ODNode::score (C++ member) vg::OrientedDistanceClusterer::ODNode::start_pos (C++ member) vg::OrientedDistanceClusterer::ODNode::~ODNode (C++ function) vg::OrientedDistanceClusterer::OrientedDistanceClusterer (C++ function), [1], [2] vg::OrientedDistanceClusterer::pair_clusters (C++ function) vg::OrientedDistanceClusterer::perform_dp (C++ function) vg::OrientedDistanceClusterer::qual_adj_aligner (C++ member) vg::OrientedDistanceClusterer::topological_order (C++ function) vg::overlap (C++ function) vg::Packer (C++ class) vg::Packer::add (C++ function) vg::Packer::as_table (C++ function) vg::Packer::bin_for_position (C++ function) vg::Packer::bin_size (C++ member) vg::Packer::close_edit_tmpfiles (C++ function) vg::Packer::collect_coverage (C++ function) vg::Packer::coverage_at_position (C++ function) vg::Packer::coverage_civ (C++ member) vg::Packer::coverage_dynamic (C++ member) vg::Packer::delim1 (C++ member) vg::Packer::delim2 (C++ member) vg::Packer::edit_count (C++ member) vg::Packer::edit_csas (C++ member) vg::Packer::edit_length (C++ member) vg::Packer::edit_tmpfile_names (C++ member) vg::Packer::edit_value (C++ function) vg::Packer::edits_at_position (C++ function) vg::Packer::ensure_edit_tmpfiles_open (C++ function) vg::Packer::escape_delim (C++ function) vg::Packer::escape_delims (C++ function) vg::Packer::get_bin_size (C++ function) vg::Packer::get_n_bins (C++ function) vg::Packer::graph_length (C++ function) vg::Packer::is_compacted (C++ member) vg::Packer::is_dynamic (C++ function) vg::Packer::load (C++ function) vg::Packer::load_from_file (C++ function) vg::Packer::make_compact (C++ function) vg::Packer::make_dynamic (C++ function) vg::Packer::merge_from_dynamic (C++ function) vg::Packer::merge_from_files (C++ function) vg::Packer::n_bins (C++ member) vg::Packer::Packer (C++ function), [1] vg::Packer::pos_key (C++ function) vg::Packer::position_in_basis (C++ function) vg::Packer::remove_edit_tmpfiles (C++ function) vg::Packer::save_to_file (C++ function) vg::Packer::serialize (C++ function) vg::Packer::show_structure (C++ function) vg::Packer::tmpfstreams (C++ member) vg::Packer::unescape_delim (C++ function) vg::Packer::unescape_delims (C++ function) vg::Packer::write_edits (C++ function), [1] vg::Packer::xgidx (C++ member) vg::Packer::~Packer (C++ function) vg::Packers (C++ class) vg::Packers::as_table (C++ function) vg::Packers::load (C++ function) vg::pair_hash_map (C++ class) vg::pair_hash_map::pair_hash_map (C++ function) vg::parse_bed_regions (C++ function), [1] vg::parse_region (C++ function) 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::PathBasedTraversalFinder (C++ class) vg::PathBasedTraversalFinder::find_traversals (C++ function) vg::PathBasedTraversalFinder::graph (C++ member) vg::PathBasedTraversalFinder::PathBasedTraversalFinder (C++ function) vg::PathBasedTraversalFinder::snarlmanager (C++ member) vg::PathBasedTraversalFinder::~PathBasedTraversalFinder (C++ function) vg::PathChunker (C++ class) vg::PathChunker::extract_gam_for_ids (C++ function) vg::PathChunker::extract_gam_for_subgraph (C++ function) vg::PathChunker::extract_id_range (C++ function) vg::PathChunker::extract_subgraph (C++ function) vg::PathChunker::gam_buffer_size (C++ member) vg::PathChunker::PathChunker (C++ function) vg::PathChunker::xg (C++ member) vg::PathChunker::~PathChunker (C++ function) vg::PathIndex (C++ class) vg::PathIndex::apply_translation (C++ function) vg::PathIndex::apply_translations (C++ function) vg::PathIndex::at_position (C++ function) vg::PathIndex::begin (C++ function) vg::PathIndex::by_id (C++ member) vg::PathIndex::by_start (C++ member) vg::PathIndex::end (C++ function) vg::PathIndex::find_position (C++ function) vg::PathIndex::iterator (C++ type) vg::PathIndex::last_node_length (C++ member) vg::PathIndex::mapping_positions (C++ member) vg::PathIndex::node_length (C++ function) vg::PathIndex::node_occurrences (C++ member) vg::PathIndex::parse_translation (C++ function) vg::PathIndex::path_contains_node (C++ function) vg::PathIndex::PathIndex (C++ function), [1], [2], [3], [4], [5] vg::PathIndex::replace_occurrence (C++ function) vg::PathIndex::round_outward (C++ function) vg::PathIndex::sequence (C++ member) vg::PathIndex::update_mapping_positions (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::PhasedGenome (C++ class) vg::PhasedGenome::add_haplotype (C++ function) vg::PhasedGenome::begin (C++ function) vg::PhasedGenome::build_indices (C++ function) vg::PhasedGenome::build_site_indices_internal (C++ function) vg::PhasedGenome::end (C++ function) vg::PhasedGenome::Haplotype (C++ class) vg::PhasedGenome::Haplotype::append_left (C++ function) vg::PhasedGenome::Haplotype::append_right (C++ function) vg::PhasedGenome::Haplotype::Haplotype (C++ function), [1] vg::PhasedGenome::Haplotype::left_telomere_node (C++ member) vg::PhasedGenome::Haplotype::right_telomere_node (C++ member) vg::PhasedGenome::Haplotype::sites (C++ member) vg::PhasedGenome::Haplotype::~Haplotype (C++ function) vg::PhasedGenome::HaplotypeNode (C++ class) vg::PhasedGenome::HaplotypeNode::HaplotypeNode (C++ function) vg::PhasedGenome::HaplotypeNode::next (C++ member) vg::PhasedGenome::HaplotypeNode::node_traversal (C++ member) vg::PhasedGenome::HaplotypeNode::prev (C++ member) vg::PhasedGenome::HaplotypeNode::~HaplotypeNode (C++ function) vg::PhasedGenome::haplotypes (C++ member) vg::PhasedGenome::insert_left (C++ function) vg::PhasedGenome::insert_right (C++ function) vg::PhasedGenome::iterator (C++ class) vg::PhasedGenome::iterator::haplo_node (C++ member) vg::PhasedGenome::iterator::haplotype_number (C++ member) vg::PhasedGenome::iterator::iterator (C++ function), [1], [2] vg::PhasedGenome::iterator::operator!= (C++ function) vg::PhasedGenome::iterator::operator* (C++ function) vg::PhasedGenome::iterator::operator++ (C++ function), [1] vg::PhasedGenome::iterator::operator= (C++ function) vg::PhasedGenome::iterator::operator== (C++ function) vg::PhasedGenome::iterator::rank (C++ member) vg::PhasedGenome::iterator::which_haplotype (C++ function) vg::PhasedGenome::iterator::~iterator (C++ function) vg::PhasedGenome::node_locations (C++ member) vg::PhasedGenome::num_haplotypes (C++ function) vg::PhasedGenome::optimal_score_on_genome (C++ function) vg::PhasedGenome::PhasedGenome (C++ function) vg::PhasedGenome::remove (C++ function) vg::PhasedGenome::set_allele (C++ function) vg::PhasedGenome::site_ends (C++ member) vg::PhasedGenome::site_starts (C++ member) vg::PhasedGenome::snarl_manager (C++ member) vg::PhasedGenome::swap_alleles (C++ function) vg::PhasedGenome::swap_label (C++ function) vg::PhasedGenome::~PhasedGenome (C++ function) vg::PhaseDuplicator (C++ class) vg::PhaseDuplicator::canonicalize (C++ function) vg::PhaseDuplicator::duplicate (C++ function) vg::PhaseDuplicator::find_border_edges (C++ function) vg::PhaseDuplicator::find_borders (C++ function) vg::PhaseDuplicator::index (C++ member) vg::PhaseDuplicator::list_haplotypes (C++ function), [1] vg::PhaseDuplicator::list_haplotypes_from (C++ function) vg::PhaseDuplicator::list_haplotypes_through (C++ function) vg::PhaseDuplicator::PhaseDuplicator (C++ function) vg::PhaseDuplicator::traverse_edge (C++ function) vg::phi (C++ function) vg::phred_geometric_mean (C++ function) vg::phred_to_logprob (C++ function) vg::phred_to_prob (C++ function) vg::Pictographs (C++ class) vg::Pictographs::char_count (C++ member) vg::Pictographs::chars (C++ member) vg::Pictographs::hashed (C++ function) vg::Pictographs::hashed_char (C++ function) vg::Pictographs::Pictographs (C++ function), [1] vg::Pictographs::random (C++ function) vg::Pictographs::rng (C++ member) vg::Pictographs::symbol_count (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::PileupAugmenter (C++ class) vg::PileupAugmenter::_augmented_edges (C++ member) vg::PileupAugmenter::_augmented_graph (C++ member) vg::PileupAugmenter::_buffer_size (C++ member) vg::PileupAugmenter::_called_edges (C++ member) vg::PileupAugmenter::_default_quality (C++ member) vg::PileupAugmenter::_deletion_supports (C++ member) vg::PileupAugmenter::_graph (C++ member) vg::PileupAugmenter::_insert_calls (C++ member) vg::PileupAugmenter::_insert_supports (C++ member) vg::PileupAugmenter::_inserted_nodes (C++ member) vg::PileupAugmenter::_insertion_supports (C++ member) vg::PileupAugmenter::_max_id (C++ member) vg::PileupAugmenter::_min_aug_support (C++ member) vg::PileupAugmenter::_node (C++ member) vg::PileupAugmenter::_node_calls (C++ member) vg::PileupAugmenter::_node_divider (C++ member) vg::PileupAugmenter::_node_supports (C++ member) vg::PileupAugmenter::_visited_nodes (C++ member) vg::PileupAugmenter::annotate_augmented_edge (C++ function) vg::PileupAugmenter::annotate_augmented_node (C++ function) vg::PileupAugmenter::annotate_augmented_nodes (C++ function) vg::PileupAugmenter::annotate_non_augmented_nodes (C++ function) vg::PileupAugmenter::apply_mapping_edits (C++ function) vg::PileupAugmenter::call_base_pileup (C++ function) vg::PileupAugmenter::call_cat (C++ function) vg::PileupAugmenter::call_edge_pileup (C++ function) vg::PileupAugmenter::call_node_pileup (C++ function) vg::PileupAugmenter::clear (C++ function) vg::PileupAugmenter::compute_top_frequencies (C++ function) vg::PileupAugmenter::create_augmented_edge (C++ function) vg::PileupAugmenter::create_node_calls (C++ function) vg::PileupAugmenter::Default_default_quality (C++ member) vg::PileupAugmenter::Default_min_aug_support (C++ member) vg::PileupAugmenter::EdgeHash (C++ type) vg::PileupAugmenter::EdgeSupHash (C++ type) vg::PileupAugmenter::Genotype (C++ type) vg::PileupAugmenter::InsertionHash (C++ type) vg::PileupAugmenter::InsertionRecord (C++ class) vg::PileupAugmenter::InsertionRecord::node (C++ member) vg::PileupAugmenter::InsertionRecord::orig_id (C++ member) vg::PileupAugmenter::InsertionRecord::orig_offset (C++ member) vg::PileupAugmenter::InsertionRecord::sup (C++ member) vg::PileupAugmenter::Log_zero (C++ member) vg::PileupAugmenter::map_path (C++ function) vg::PileupAugmenter::map_paths (C++ function) vg::PileupAugmenter::missing_call (C++ function) vg::PileupAugmenter::NodeOffSide (C++ type) vg::PileupAugmenter::PileupAugmenter (C++ function) vg::PileupAugmenter::ref_call (C++ function) vg::PileupAugmenter::safe_log (C++ function) vg::PileupAugmenter::total_base_quality (C++ function) vg::PileupAugmenter::update_augmented_graph (C++ function) vg::PileupAugmenter::verify_path (C++ function) vg::PileupAugmenter::write_augmented_graph (C++ function) vg::PileupAugmenter::~PileupAugmenter (C++ function) 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::pointerfy (C++ function) vg::poisson_prob_ln (C++ function) vg::pos_t (C++ type) vg::Position (C++ class) vg::Position::is_reverse (C++ member) vg::Position::name (C++ member) vg::Position::node_id (C++ member) vg::Position::offset (C++ member) vg::position_at (C++ function) vg::pow_ln (C++ function) vg::primitive_roots_of_unity (C++ member) 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::init_mapping_quality (C++ function) vg::QualAdjAligner::max_qual_score (C++ member) vg::QualAdjAligner::scale_factor (C++ member) vg::QualAdjAligner::~QualAdjAligner (C++ function) vg::quality_char_to_short (C++ function) vg::quality_short_to_char (C++ function) vg::query_overlap (C++ function) vg::range_vector (C++ function) vg::ReadFilter (C++ class) vg::ReadFilter::append_regions (C++ member) 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_end_matches (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_end_matches (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::ReadRestrictedTraversalFinder (C++ class) vg::ReadRestrictedTraversalFinder::find_traversals (C++ function) vg::ReadRestrictedTraversalFinder::graph (C++ member) vg::ReadRestrictedTraversalFinder::max_path_search_steps (C++ member) vg::ReadRestrictedTraversalFinder::min_recurrence (C++ member) vg::ReadRestrictedTraversalFinder::ReadRestrictedTraversalFinder (C++ function) vg::ReadRestrictedTraversalFinder::reads_by_name (C++ member) vg::ReadRestrictedTraversalFinder::snarl_manager (C++ member) vg::ReadRestrictedTraversalFinder::~ReadRestrictedTraversalFinder (C++ function) vg::Region (C++ class) vg::Region::end (C++ member) vg::Region::seq (C++ member) vg::Region::start (C++ member) vg::remove_duplicate_edges (C++ function) vg::remove_duplicate_nodes (C++ function) vg::remove_duplicates (C++ function) vg::remove_orphan_edges (C++ function) vg::ReplaceLocalHaplotypeCommand (C++ class) vg::ReplaceLocalHaplotypeCommand::deletions (C++ member) vg::ReplaceLocalHaplotypeCommand::execute (C++ function) vg::ReplaceLocalHaplotypeCommand::insertions (C++ member) vg::ReplaceLocalHaplotypeCommand::~ReplaceLocalHaplotypeCommand (C++ function) vg::ReplaceSnarlHaplotypeCommand (C++ class) vg::ReplaceSnarlHaplotypeCommand::execute (C++ function) vg::ReplaceSnarlHaplotypeCommand::haplotype (C++ member) vg::ReplaceSnarlHaplotypeCommand::lane (C++ member) vg::ReplaceSnarlHaplotypeCommand::snarl (C++ member) vg::ReplaceSnarlHaplotypeCommand::~ReplaceSnarlHaplotypeCommand (C++ function) vg::RepresentativeTraversalFinder (C++ class) vg::RepresentativeTraversalFinder::augmented (C++ member) vg::RepresentativeTraversalFinder::bfs_left (C++ function) vg::RepresentativeTraversalFinder::bfs_right (C++ function) vg::RepresentativeTraversalFinder::bp_length (C++ function) vg::RepresentativeTraversalFinder::find_backbone (C++ function) vg::RepresentativeTraversalFinder::find_bubble (C++ function) vg::RepresentativeTraversalFinder::find_traversals (C++ function) vg::RepresentativeTraversalFinder::get_index (C++ member) vg::RepresentativeTraversalFinder::max_bubble_paths (C++ member) vg::RepresentativeTraversalFinder::max_depth (C++ member) vg::RepresentativeTraversalFinder::max_width (C++ member) vg::RepresentativeTraversalFinder::min_support_in_path (C++ function) vg::RepresentativeTraversalFinder::RepresentativeTraversalFinder (C++ function) vg::RepresentativeTraversalFinder::snarl_manager (C++ member) vg::RepresentativeTraversalFinder::verbose (C++ member) vg::RepresentativeTraversalFinder::~RepresentativeTraversalFinder (C++ function) vg::rev_comp_multipath_alignment (C++ function) vg::rev_comp_multipath_alignment_in_place (C++ function) vg::rev_comp_subpath (C++ function) vg::reverse (C++ function), [1], [2] vg::reverse_complement (C++ function), [1] vg::reverse_complement_alignment (C++ function) vg::reverse_complement_alignment_in_place (C++ function) vg::reverse_complement_alignments (C++ function) vg::reverse_complement_edit (C++ function) vg::reverse_complement_in_place (C++ function) vg::reverse_complement_mapping (C++ function) vg::reverse_complement_mapping_in_place (C++ function) vg::reverse_complement_path (C++ function) vg::reverse_complement_path_in_place (C++ function) vg::run_benchmark (C++ function), [1] 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_to_graph (C++ function) vg::Sampler::alignment_to_path (C++ function) vg::Sampler::alignment_with_error (C++ function) vg::Sampler::edge_cache (C++ member) vg::Sampler::forward_only (C++ member) vg::Sampler::is_valid (C++ function) vg::Sampler::mutate (C++ function) vg::Sampler::mutate_edit (C++ function) vg::Sampler::next_pos_chars (C++ function) vg::Sampler::no_Ns (C++ member) vg::Sampler::node_cache (C++ member) vg::Sampler::node_length (C++ function) vg::Sampler::nonce (C++ member) vg::Sampler::path_sampler (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::set_source_paths (C++ function) vg::Sampler::source_paths (C++ member) vg::Sampler::xgidx (C++ member) vg::set_intersection (C++ function) vg::sha1head (C++ function) vg::sha1sum (C++ function) vg::ShuffledPairs (C++ class) vg::ShuffledPairs::begin (C++ function) vg::ShuffledPairs::const_iterator (C++ type) vg::ShuffledPairs::end (C++ function) vg::ShuffledPairs::iterator (C++ class) vg::ShuffledPairs::iterator::iteratee (C++ member) vg::ShuffledPairs::iterator::iterator (C++ function), [1] vg::ShuffledPairs::iterator::operator!= (C++ function) vg::ShuffledPairs::iterator::operator* (C++ function) vg::ShuffledPairs::iterator::operator++ (C++ function) vg::ShuffledPairs::iterator::operator= (C++ function) vg::ShuffledPairs::iterator::operator== (C++ function) vg::ShuffledPairs::iterator::permutation_idx (C++ member) vg::ShuffledPairs::iterator::permuted (C++ member) vg::ShuffledPairs::larger_prime (C++ member) vg::ShuffledPairs::num_items (C++ member) vg::ShuffledPairs::num_pairs (C++ member) vg::ShuffledPairs::primitive_root (C++ member) vg::ShuffledPairs::ShuffledPairs (C++ function) vg::Side2Component (C++ type) vg::SideSet (C++ type) vg::signature (C++ function), [1] vg::SimpleConsistencyCalculator (C++ class) vg::SimpleConsistencyCalculator::calculate_consistency (C++ function) vg::SimpleConsistencyCalculator::~SimpleConsistencyCalculator (C++ function) vg::SimpleTraversalSupportCalculator (C++ class) vg::SimpleTraversalSupportCalculator::calculate_supports (C++ function) vg::SimpleTraversalSupportCalculator::~SimpleTraversalSupportCalculator (C++ function) vg::Simplifier (C++ class) vg::Simplifier::drop_hairpin_paths (C++ member) vg::Simplifier::features (C++ member) vg::Simplifier::graph (C++ member) vg::Simplifier::max_iterations (C++ member) vg::Simplifier::min_size (C++ member) vg::Simplifier::Simplifier (C++ function) vg::Simplifier::simplify (C++ function) vg::Simplifier::simplify_once (C++ function) vg::Simplifier::site_manager (C++ member) vg::Simplifier::traversal_finder (C++ member) vg::simplify (C++ function), [1], [2] vg::slope (C++ function) vg::Snarl (C++ class) vg::Snarl::directed_acyclic_net_graph (C++ member) vg::Snarl::end (C++ member) vg::Snarl::end_self_reachable (C++ member) vg::Snarl::name (C++ member) vg::Snarl::parent (C++ member) vg::Snarl::start (C++ member) vg::Snarl::start_end_reachable (C++ member) vg::Snarl::start_self_reachable (C++ member) vg::Snarl::type (C++ member) vg::SnarlFinder (C++ class) vg::SnarlFinder::find_snarls (C++ function) vg::SnarlFinder::~SnarlFinder (C++ function) vg::SnarlManager (C++ class) vg::SnarlManager::add_chain (C++ function) vg::SnarlManager::add_snarl (C++ function) vg::SnarlManager::build_indexes (C++ function) vg::SnarlManager::chain_of (C++ function) vg::SnarlManager::chains_of (C++ function) vg::SnarlManager::child_chains (C++ member) vg::SnarlManager::children (C++ member) vg::SnarlManager::children_of (C++ function) vg::SnarlManager::compute_chains (C++ function) vg::SnarlManager::deep_contents (C++ function) vg::SnarlManager::flip (C++ function) vg::SnarlManager::for_each_snarl_parallel (C++ function) vg::SnarlManager::for_each_snarl_preorder (C++ function) vg::SnarlManager::for_each_top_level_snarl (C++ function) vg::SnarlManager::for_each_top_level_snarl_parallel (C++ function) vg::SnarlManager::in_nontrivial_chain (C++ function) vg::SnarlManager::into_which_snarl (C++ function), [1] vg::SnarlManager::is_leaf (C++ function) vg::SnarlManager::is_root (C++ function) vg::SnarlManager::key_form (C++ function) vg::SnarlManager::key_t (C++ type) vg::SnarlManager::manage (C++ function) vg::SnarlManager::net_graph_of (C++ function) vg::SnarlManager::next_snarl (C++ function) vg::SnarlManager::operator= (C++ function), [1] vg::SnarlManager::parent (C++ member) vg::SnarlManager::parent_chain (C++ member) vg::SnarlManager::parent_of (C++ function) vg::SnarlManager::prev_snarl (C++ function) vg::SnarlManager::root_chains (C++ member) vg::SnarlManager::roots (C++ member) vg::SnarlManager::self (C++ member) vg::SnarlManager::shallow_contents (C++ function) vg::SnarlManager::snarl_boundary_index (C++ function) vg::SnarlManager::snarl_end_index (C++ function) vg::SnarlManager::snarl_into (C++ member) vg::SnarlManager::snarl_sharing_end (C++ function) vg::SnarlManager::snarl_sharing_start (C++ function) vg::SnarlManager::snarl_start_index (C++ function) vg::SnarlManager::SnarlManager (C++ function), [1], [2], [3], [4] vg::SnarlManager::snarls (C++ member) vg::SnarlManager::top_level_snarls (C++ function) vg::SnarlManager::visits_left (C++ function) vg::SnarlManager::visits_right (C++ function) vg::SnarlManager::~SnarlManager (C++ function) vg::SnarlState (C++ class) vg::SnarlState::append (C++ function) vg::SnarlState::dump (C++ function) vg::SnarlState::erase (C++ function) vg::SnarlState::graph (C++ member) vg::SnarlState::haplotypes (C++ member) vg::SnarlState::insert (C++ function), [1] vg::SnarlState::net_node_lanes (C++ member) vg::SnarlState::size (C++ function) vg::SnarlState::SnarlState (C++ function) vg::SnarlState::swap (C++ function) vg::SnarlState::trace (C++ function) vg::SnarlTraversal (C++ class) vg::SnarlTraversal::name (C++ member) vg::SnarlTraversal::visits (C++ member) vg::SnarlType (C++ type) vg::softclip_end (C++ function), [1] vg::softclip_start (C++ function), [1] vg::sort_by_id (C++ function) vg::sort_by_id_dedup_and_clean (C++ function) vg::sort_edges_by_id (C++ function) vg::sort_nodes_by_id (C++ function) vg::spaced_primes (C++ member) vg::split_delims (C++ function), [1] vg::SRPE (C++ class) vg::SRPE::aln_to_bseq (C++ function) vg::SRPE::aln_to_mate (C++ member) vg::SRPE::assemble (C++ function), [1], [2] vg::SRPE::call_svs (C++ function) vg::SRPE::call_svs_paired_end (C++ function) vg::SRPE::call_svs_split_read (C++ function) vg::SRPE::depth (C++ member) vg::SRPE::discordance_score (C++ function) vg::SRPE::ff (C++ member) vg::SRPE::graph (C++ member) vg::SRPE::intervals (C++ member) vg::SRPE::max_reads (C++ member) vg::SRPE::name_to_aln (C++ member) vg::SRPE::overlapping_refs (C++ member) vg::SRPE::pindexes (C++ member) vg::SRPE::ref_names (C++ member) 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::start_backward (C++ function) vg::stdev (C++ function), [1] vg::strand_bias (C++ function) vg::StrandSupport (C++ class) vg::StrandSupport::fs (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::qual (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::sub_overlaps_of_first_aln (C++ function) vg::subcommand (C++ type) vg::subcommand::CommandCategory (C++ type) vg::subcommand::DEVELOPMENT (C++ class) vg::subcommand::operator<< (C++ function) vg::subcommand::PIPELINE (C++ class) vg::subcommand::Subcommand (C++ class) vg::subcommand::Subcommand::category (C++ member) vg::subcommand::Subcommand::description (C++ member) vg::subcommand::Subcommand::for_each (C++ function), [1] vg::subcommand::Subcommand::get (C++ function) vg::subcommand::Subcommand::get_category (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_priority (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::priority (C++ member) vg::subcommand::Subcommand::Subcommand (C++ function), [1], [2] vg::subcommand::TOOLKIT (C++ class) vg::subcommand::WIDGET (C++ class) vg::Subpath (C++ class) vg::Subpath::next (C++ member) vg::Subpath::path (C++ member) vg::Subpath::score (C++ member) vg::SuffixTree (C++ class) vg::SuffixTree::active_point_string (C++ function) vg::SuffixTree::begin (C++ member) vg::SuffixTree::end (C++ member) vg::SuffixTree::get_char (C++ function) vg::SuffixTree::label_string (C++ function) vg::SuffixTree::longest_overlap (C++ function), [1] vg::SuffixTree::node_string (C++ function) vg::SuffixTree::nodes (C++ member) vg::SuffixTree::partial_tree_to_string (C++ function) vg::SuffixTree::root (C++ member) vg::SuffixTree::STNode (C++ class) vg::SuffixTree::STNode::children (C++ member) vg::SuffixTree::STNode::final_index (C++ function) vg::SuffixTree::STNode::first (C++ member) vg::SuffixTree::STNode::last (C++ member) vg::SuffixTree::STNode::length (C++ function) vg::SuffixTree::STNode::STNode (C++ function) vg::SuffixTree::STNode::~STNode (C++ function) vg::SuffixTree::substring_locations (C++ function), [1] vg::SuffixTree::suffix_links_string (C++ function) vg::SuffixTree::SuffixTree (C++ function) vg::SuffixTree::to_string (C++ function) vg::SuffixTree::~SuffixTree (C++ function) vg::sum (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::support_max (C++ function) vg::support_min (C++ function) vg::SupportAugmentedGraph (C++ class) vg::SupportAugmentedGraph::clear (C++ function) vg::SupportAugmentedGraph::edge_supports (C++ member) vg::SupportAugmentedGraph::get_support (C++ function), [1] vg::SupportAugmentedGraph::has_supports (C++ function) vg::SupportAugmentedGraph::load_supports (C++ function) vg::SupportAugmentedGraph::node_supports (C++ member) vg::SupportAugmentedGraph::write_supports (C++ function) vg::SupportCaller (C++ class) vg::SupportCaller::average_support_switch_threshold (C++ member) vg::SupportCaller::call (C++ function) vg::SupportCaller::call_other_by_coverage (C++ member) vg::SupportCaller::contig_name_overrides (C++ member) vg::SupportCaller::convert_to_vcf (C++ member) vg::SupportCaller::expected_coverage (C++ member) vg::SupportCaller::find_best_traversals (C++ function) vg::SupportCaller::find_path (C++ function) vg::SupportCaller::get_traversal_supports_and_sizes (C++ function) vg::SupportCaller::is_reference (C++ function), [1] vg::SupportCaller::length_overrides (C++ member) vg::SupportCaller::locus_buffer_size (C++ member) vg::SupportCaller::max_bubble_paths (C++ member) vg::SupportCaller::max_dp_for_filter (C++ member) vg::SupportCaller::max_dp_multiple_for_filter (C++ member) vg::SupportCaller::max_het_bias (C++ member) vg::SupportCaller::max_indel_het_bias (C++ member) vg::SupportCaller::max_indel_ma_bias (C++ member) vg::SupportCaller::max_local_dp_multiple_for_filter (C++ member) vg::SupportCaller::max_ref_het_bias (C++ member) vg::SupportCaller::max_search_depth (C++ member) vg::SupportCaller::max_search_width (C++ member) vg::SupportCaller::min_ad_log_likelihood_for_filter (C++ member) vg::SupportCaller::min_fraction_for_call (C++ member) vg::SupportCaller::min_mad_for_filter (C++ member) vg::SupportCaller::min_total_support_for_call (C++ member) vg::SupportCaller::PrimaryPath (C++ class) vg::SupportCaller::PrimaryPath::binned_support (C++ member) vg::SupportCaller::PrimaryPath::get_average_support (C++ function), [1] vg::SupportCaller::PrimaryPath::get_bin (C++ function) vg::SupportCaller::PrimaryPath::get_bin_index (C++ function) vg::SupportCaller::PrimaryPath::get_index (C++ function), [1] vg::SupportCaller::PrimaryPath::get_max_bin (C++ function) vg::SupportCaller::PrimaryPath::get_min_bin (C++ function) vg::SupportCaller::PrimaryPath::get_name (C++ function) vg::SupportCaller::PrimaryPath::get_support_at (C++ function) vg::SupportCaller::PrimaryPath::get_total_bins (C++ function) vg::SupportCaller::PrimaryPath::get_total_support (C++ function) vg::SupportCaller::PrimaryPath::index (C++ member) vg::SupportCaller::PrimaryPath::max_bin (C++ member) vg::SupportCaller::PrimaryPath::min_bin (C++ member) vg::SupportCaller::PrimaryPath::name (C++ member) vg::SupportCaller::PrimaryPath::PrimaryPath (C++ function) vg::SupportCaller::PrimaryPath::ref_bin_size (C++ member) vg::SupportCaller::PrimaryPath::total_support (C++ member) vg::SupportCaller::ref_bin_size (C++ member) vg::SupportCaller::ref_path_names (C++ member) vg::SupportCaller::sample_name (C++ member) vg::SupportCaller::support_file_name (C++ member) vg::SupportCaller::support_quality (C++ function) vg::SupportCaller::support_val (C++ member) vg::SupportCaller::SupportCaller (C++ function) vg::SupportCaller::use_average_support (C++ member) vg::SupportCaller::use_support_count (C++ member) vg::SupportCaller::variant_offset (C++ member) vg::SupportCaller::verbose (C++ member) vg::SupportCaller::write_trivial_calls (C++ member) vg::SwapHaplotypesCommand (C++ class) vg::SwapHaplotypesCommand::execute (C++ function) vg::SwapHaplotypesCommand::telomere_pair (C++ member) vg::SwapHaplotypesCommand::to_swap (C++ member) vg::SwapHaplotypesCommand::~SwapHaplotypesCommand (C++ function) vg::tmpfilename (C++ function), [1] vg::to_left_side (C++ function) vg::to_length (C++ function) vg::to_length_after_pos (C++ function) vg::to_length_before_pos (C++ function) vg::to_mapping (C++ function), [1] vg::to_multipath_alignment (C++ function) vg::to_node_traversal (C++ function), [1] vg::to_rev_node_traversal (C++ function), [1] vg::to_rev_visit (C++ function) vg::to_right_side (C++ function) vg::to_string_ss (C++ function) vg::to_vcf_genotype (C++ function) vg::to_visit (C++ function), [1], [2], [3] vg::topologically_order_subpaths (C++ function) vg::total (C++ function) vg::totalSup (C++ function) vg::toUppercase (C++ function) vg::trace_traversal (C++ function) vg::transfer_boundary_info (C++ function) vg::transfer_read_metadata (C++ function), [1], [2] vg::translate_node_ids (C++ function) vg::translate_nodes (C++ function) vg::translate_oriented_node_ids (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::has_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], [6] 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 (C++ class) vg::UNARY (C++ class) vg::UNCLASSIFIED (C++ class) vg::UnionFind (C++ class) vg::UnionFind::all_groups (C++ function) vg::UnionFind::current_state (C++ function) vg::UnionFind::find_group (C++ function) vg::UnionFind::group (C++ function) vg::UnionFind::group_size (C++ function) vg::UnionFind::size (C++ function) vg::UnionFind::uf_nodes (C++ member) vg::UnionFind::UFNode (C++ class) vg::UnionFind::UFNode::children (C++ member) vg::UnionFind::UFNode::head (C++ member) vg::UnionFind::UFNode::rank (C++ member) vg::UnionFind::UFNode::size (C++ member) vg::UnionFind::UFNode::UFNode (C++ function) vg::UnionFind::UFNode::~UFNode (C++ function) vg::UnionFind::union_groups (C++ function) vg::UnionFind::UnionFind (C++ function) vg::UnionFind::~UnionFind (C++ function) vg::unittest (C++ type) vg::unittest::run_unit_tests (C++ function) vg::variant_recall (C++ function) vg::VariantAdder (C++ class) vg::VariantAdder::add_variants (C++ function) vg::VariantAdder::align_ns (C++ function) vg::VariantAdder::aligner (C++ member) vg::VariantAdder::doubling_steps (C++ member) vg::VariantAdder::edge_max (C++ member) vg::VariantAdder::filter_local_variants (C++ function) vg::VariantAdder::flank_range (C++ member) vg::VariantAdder::get_center (C++ function) vg::VariantAdder::get_center_and_radius (C++ function) vg::VariantAdder::get_radius (C++ function) vg::VariantAdder::get_unique_haplotypes (C++ function) vg::VariantAdder::graph (C++ member) vg::VariantAdder::haplotype_to_string (C++ function) vg::VariantAdder::ignore_missing_contigs (C++ member) vg::VariantAdder::kmer_size (C++ member) vg::VariantAdder::large_alignment_band_padding (C++ member) vg::VariantAdder::mapper_alignment_cutoff (C++ member) vg::VariantAdder::max_context_radius (C++ member) vg::VariantAdder::min_score_factor (C++ member) vg::VariantAdder::path_names (C++ member) vg::VariantAdder::pinned_tail_size (C++ member) vg::VariantAdder::print_updates (C++ member) vg::VariantAdder::skip_structural_duplications (C++ member) vg::VariantAdder::smart_align (C++ function) vg::VariantAdder::subgraph_prune (C++ member) vg::VariantAdder::sync (C++ member) vg::VariantAdder::thin_alignment_cutoff (C++ member) vg::VariantAdder::variant_range (C++ member) vg::VariantAdder::VariantAdder (C++ function) vg::VariantAdder::whole_alignment_cutoff (C++ member) 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), [1] 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::apply_orientation (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_edge_indexes_no_init_size (C++ function) vg::VG::build_gcsa_lcp (C++ function) vg::VG::build_indexes (C++ function) vg::VG::build_indexes_no_init_size (C++ function) vg::VG::build_node_indexes (C++ function) vg::VG::build_node_indexes_no_init_size (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], [4] vg::VG::create_handle (C++ function) 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], [3] vg::VG::destroy_handle (C++ function) 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_handle (C++ function) 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::edit_fast (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_context_by_length (C++ function) vg::VG::expand_context_by_steps (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 (C++ function) vg::VG::flip_doubly_reversed_edges (C++ function) vg::VG::follow_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_handle (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_handle (C++ function) vg::VG::get_id (C++ function) vg::VG::get_is_reverse (C++ function) vg::VG::get_length (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_path_edges (C++ function) vg::VG::get_sequence (C++ function) 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::HIGH_BIT (C++ member) vg::VG::identically_oriented_sibling_sets (C++ function) vg::VG::identity_translation (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_directed_acyclic (C++ function) vg::VG::is_head_node (C++ function), [1] vg::VG::is_self_looping (C++ function) vg::VG::is_single_stranded (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::lazy_sort (C++ function) vg::VG::left_degree (C++ function) vg::VG::length (C++ function) vg::VG::likelihoods (C++ function) vg::VG::LOW_BITS (C++ member) 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_size (C++ function) 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::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::remove_path (C++ function) vg::VG::resize_indexes (C++ function) vg::VG::reverse_complement_graph (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::split_strands (C++ function) vg::VG::start_degree (C++ function) vg::VG::strongly_connected_components (C++ function) vg::VG::swap_handles (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::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::variant_to_traversal (C++ member) vg::VG::VG (C++ function), [1], [2], [3], [4], [5] 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_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::Visit (C++ class) vg::Visit::backward (C++ member) vg::Visit::node_id (C++ member) vg::Visit::snarl (C++ member) vg::vpmax (C++ function) vg::WindowedVcfBuffer (C++ class) vg::WindowedVcfBuffer::cached_genotypes (C++ member) vg::WindowedVcfBuffer::current (C++ member) vg::WindowedVcfBuffer::decompose_genotype_fast (C++ function) vg::WindowedVcfBuffer::get (C++ function) vg::WindowedVcfBuffer::get_nonoverlapping (C++ function) vg::WindowedVcfBuffer::get_parsed_genotypes (C++ function) vg::WindowedVcfBuffer::has_tabix (C++ function) vg::WindowedVcfBuffer::map_order_to_original (C++ member) vg::WindowedVcfBuffer::next (C++ function) vg::WindowedVcfBuffer::operator= (C++ function) vg::WindowedVcfBuffer::reader (C++ member) vg::WindowedVcfBuffer::set_region (C++ function) vg::WindowedVcfBuffer::variants_after (C++ member) vg::WindowedVcfBuffer::variants_before (C++ member) vg::WindowedVcfBuffer::window_size (C++ member) vg::WindowedVcfBuffer::WindowedVcfBuffer (C++ function), [1] vg::wrap_text (C++ function) vg::write_alignment_to_file (C++ function) vg::write_alignments (C++ function) vg::write_vcf_header (C++ function) vg::xg_cached_distance (C++ function) vg::xg_cached_edges_of (C++ function) vg::xg_cached_edges_on_end (C++ function) vg::xg_cached_edges_on_start (C++ function) vg::xg_cached_next_pos (C++ function) vg::xg_cached_next_pos_chars (C++ function) vg::xg_cached_node (C++ function) vg::xg_cached_node_length (C++ function) vg::xg_cached_node_sequence (C++ function) vg::xg_cached_node_start (C++ function) vg::xg_cached_pos_char (C++ function) vg::xg_cached_positions_bp_from (C++ function) vg::xg_distance (C++ function) vg::xg_edges_on_end (C++ function) vg::xg_edges_on_start (C++ function) vg::xg_next_pos (C++ function) vg::xg_next_pos_chars (C++ function) vg::xg_node (C++ function) vg::xg_node_length (C++ function) vg::xg_node_sequence (C++ function) vg::xg_node_start (C++ function) vg::xg_pos_char (C++ function) vg::xg_positions_bp_from (C++ function) VG_BIN2ASCII_H_INCLUDED (C macro) VG_GIT_VERSION (C macro) vg_help (C++ function) VG_HOMOGENIZEER (C macro)

X

xg (C++ type) xg::arrive_by_reverse (C++ function) xg::depart_by_reverse (C++ function) xg::deserialize (C++ function) xg::dna3bit (C++ function) xg::edges_equivalent (C++ function) xg::extract_pos (C++ function) xg::extract_pos_substr (C++ function) xg::hash_map (C++ class) xg::hash_map::hash_map (C++ function), [1] xg::hash_map<K *, V> (C++ class) xg::hash_set (C++ class) xg::hash_set::hash_set (C++ function), [1] xg::hash_set<K *> (C++ class) xg::id_t (C++ type) xg::make_edge (C++ function) xg::make_side (C++ function) xg::make_trav (C++ function) xg::new_mapping (C++ function) xg::pair_hash_map (C++ class) xg::pair_hash_map::pair_hash_map (C++ function) xg::pair_hash_set (C++ class) xg::pair_hash_set::pair_hash_set (C++ function) xg::parse_region (C++ function) xg::relative_orientation (C++ function) xg::revdna3bit (C++ function) xg::reverse_complement (C++ function), [1] xg::serialize (C++ function) xg::side_id (C++ function) xg::side_is_end (C++ function) xg::side_t (C++ type) xg::string_hash_map (C++ class) xg::string_hash_map::string_hash_map (C++ function) xg::string_hash_set (C++ class) xg::string_hash_set::string_hash_set (C++ function) xg::to_text (C++ function) xg::trav_id (C++ function) xg::trav_is_rev (C++ function) xg::trav_rank (C++ function) xg::trav_t (C++ type) xg::XG (C++ class) xg::XG::add_paths_to_graph (C++ function) xg::XG::bs_arrays (C++ member) xg::XG::bs_bake (C++ function) xg::XG::bs_dump (C++ function) xg::XG::bs_get (C++ function) xg::XG::bs_insert (C++ function) xg::XG::BS_NULL (C++ member) xg::XG::bs_rank (C++ function) xg::XG::BS_SEPARATOR (C++ member) xg::XG::bs_set (C++ function) xg::XG::bs_single_array (C++ member) xg::XG::build (C++ function) xg::XG::canonicalize (C++ function) xg::XG::closest_shared_path_oriented_distance (C++ function) xg::XG::component_path_set_of_path (C++ member) xg::XG::component_path_sets (C++ member) xg::XG::count_matches (C++ function), [1] xg::XG::create_succinct_component_path_sets (C++ function) xg::XG::destination_t (C++ type) xg::XG::distance_in_paths (C++ function) xg::XG::do_edges (C++ function) xg::XG::edge_count (C++ member) xg::XG::edge_filter (C++ function) xg::XG::edge_from_encoding (C++ function) xg::XG::edge_graph_idx (C++ function) xg::XG::edge_type (C++ function), [1] xg::XG::edges_from (C++ function) xg::XG::edges_of (C++ function) xg::XG::edges_on_end (C++ function) xg::XG::edges_on_start (C++ function) xg::XG::edges_to (C++ function) xg::XG::end_marker (C++ member) xg::XG::expand_context (C++ function) xg::XG::expand_context_by_length (C++ function) xg::XG::expand_context_by_steps (C++ function) xg::XG::extend_search (C++ function), [1] xg::XG::extract_thread (C++ function), [1] xg::XG::extract_threads (C++ function) xg::XG::extract_threads_matching (C++ function) xg::XG::flip (C++ function) xg::XG::follow_edges (C++ function) xg::XG::for_each_handle (C++ function) xg::XG::for_path_range (C++ function) xg::XG::from_callback (C++ function) xg::XG::from_graph (C++ function) xg::XG::from_stream (C++ function) xg::XG::g_bv (C++ member) xg::XG::g_bv_rank (C++ member) xg::XG::g_bv_select (C++ member) xg::XG::G_EDGE_LENGTH (C++ member) xg::XG::G_EDGE_OFFSET_OFFSET (C++ member) xg::XG::G_EDGE_TYPE_OFFSET (C++ member) xg::XG::g_iv (C++ member) xg::XG::G_NODE_FROM_COUNT_OFFSET (C++ member) xg::XG::G_NODE_HEADER_LENGTH (C++ member) xg::XG::G_NODE_ID_OFFSET (C++ member) xg::XG::G_NODE_LENGTH_OFFSET (C++ member) xg::XG::G_NODE_SEQ_START_OFFSET (C++ member) xg::XG::G_NODE_TO_COUNT_OFFSET (C++ member) xg::XG::get_connected_nodes (C++ function) xg::XG::get_handle (C++ function) xg::XG::get_id (C++ function) xg::XG::get_id_range (C++ function) xg::XG::get_id_range_by_length (C++ function) xg::XG::get_is_reverse (C++ function) xg::XG::get_length (C++ function) xg::XG::get_path (C++ function) xg::XG::get_path_range (C++ function) xg::XG::get_sequence (C++ function) xg::XG::graph_context_g (C++ function) xg::XG::graph_context_id (C++ function) xg::XG::graph_pos_at_path_position (C++ function) xg::XG::h_civ (C++ member) xg::XG::h_iv (C++ member) xg::XG::has_edge (C++ function), [1] xg::XG::has_node (C++ function) xg::XG::HIGH_BIT (C++ member) xg::XG::i_iv (C++ member) xg::XG::id_rev_to_side (C++ function) xg::XG::id_to_rank (C++ function) xg::XG::idify_graph (C++ function) xg::XG::index_component_path_sets (C++ function) xg::XG::insert_thread (C++ function) xg::XG::insert_threads_into_dag (C++ function)

xg::XG::jump_along_closest_path (C++ function) xg::XG::load (C++ function) xg::XG::LOW_BITS (C++ member) xg::XG::mapping_at_path_position (C++ function) xg::XG::max_id (C++ member) xg::XG::MAX_INPUT_VERSION (C++ member) xg::XG::max_node_rank (C++ function) xg::XG::max_path_rank (C++ function) xg::XG::memoized_get_handle (C++ function) xg::XG::memoized_oriented_paths_of_node (C++ function) xg::XG::min_approx_path_distance (C++ function) xg::XG::min_distance_in_paths (C++ function) xg::XG::min_id (C++ member) xg::XG::names_str (C++ member) xg::XG::nearest_offsets_in_paths (C++ function) xg::XG::nearest_path_node (C++ function) xg::XG::neighborhood (C++ function) xg::XG::next_path_position (C++ function) xg::XG::node (C++ function) xg::XG::node_at_path_position (C++ function) xg::XG::node_at_seq_pos (C++ function) xg::XG::node_count (C++ member) xg::XG::node_graph_idx (C++ function) xg::XG::node_height (C++ function) xg::XG::node_length (C++ function) xg::XG::node_mappings (C++ function) xg::XG::node_occs_in_path (C++ function), [1] xg::XG::node_ranks_in_path (C++ function), [1] xg::XG::node_sequence (C++ function) xg::XG::node_size (C++ function) xg::XG::node_start (C++ function) xg::XG::node_start_at_path_position (C++ function) xg::XG::node_subgraph_g (C++ function) xg::XG::node_subgraph_id (C++ function) xg::XG::np_bv (C++ member) xg::XG::np_bv_rank (C++ member) xg::XG::np_bv_select (C++ member) xg::XG::np_iv (C++ member) xg::XG::offsets_in_paths (C++ function) xg::XG::operator= (C++ function), [1] xg::XG::oriented_paths_of_node (C++ function) xg::XG::OUTPUT_VERSION (C++ member) xg::XG::path (C++ function) xg::XG::path_contains_node (C++ function) xg::XG::path_count (C++ member) xg::XG::path_length (C++ function), [1] xg::XG::path_name (C++ function) xg::XG::path_rank (C++ function) xg::XG::paths (C++ member) xg::XG::paths_of_node (C++ function) xg::XG::paths_on_same_component (C++ function) xg::XG::pi_iv (C++ member) xg::XG::pn_bv (C++ member) xg::XG::pn_bv_rank (C++ member) xg::XG::pn_bv_select (C++ member) xg::XG::pn_csa (C++ member) xg::XG::pn_iv (C++ member) xg::XG::pos_char (C++ function) xg::XG::pos_substr (C++ function) xg::XG::position_in_path (C++ function), [1] xg::XG::position_in_paths (C++ function) xg::XG::r_iv (C++ member) xg::XG::rank_select_int_vector (C++ type) xg::XG::rank_to_id (C++ function) xg::XG::s_bv (C++ member) xg::XG::s_bv_rank (C++ member) xg::XG::s_bv_select (C++ member) xg::XG::s_iv (C++ member) xg::XG::select_continuing (C++ function) xg::XG::select_starting (C++ function) xg::XG::seq_length (C++ member) xg::XG::sequence_bit_size (C++ function) xg::XG::sequence_data (C++ function) xg::XG::serialize (C++ function) xg::XG::set_thread_names (C++ function) xg::XG::side_thread_wt (C++ member) xg::XG::side_to_id_rev (C++ function) xg::XG::start_marker (C++ member) xg::XG::target_alignment (C++ function) xg::XG::thread_name (C++ function) xg::XG::thread_start (C++ function), [1] xg::XG::thread_starting_at (C++ function) xg::XG::thread_t (C++ type) xg::XG::ThreadMapping (C++ class) xg::XG::ThreadMapping::is_reverse (C++ member) xg::XG::ThreadMapping::node_id (C++ member) xg::XG::ThreadMapping::operator< (C++ function) xg::XG::threads_named_starting (C++ function) xg::XG::threads_starting_on_side (C++ function) xg::XG::ThreadSearchState (C++ class) xg::XG::ThreadSearchState::count (C++ function) xg::XG::ThreadSearchState::current_side (C++ member) xg::XG::ThreadSearchState::is_empty (C++ function) xg::XG::ThreadSearchState::range_end (C++ member) xg::XG::ThreadSearchState::range_start (C++ member) xg::XG::tin_civ (C++ member) xg::XG::tio_civ (C++ member) xg::XG::tn_bake (C++ function) xg::XG::tn_cbv (C++ member) xg::XG::tn_cbv_rank (C++ member) xg::XG::tn_cbv_select (C++ member) xg::XG::tn_csa (C++ member) xg::XG::ts_civ (C++ member) xg::XG::ts_iv (C++ member) xg::XG::unpack_succinct_component_path_sets (C++ function) xg::XG::where_to (C++ function), [1] xg::XG::XG (C++ function), [1], [2], [3], [4], [5] xg::XG::~XG (C++ function) xg::XGFormatError (C++ class) xg::XGPath (C++ class) xg::XGPath::directions (C++ member) xg::XGPath::ids (C++ member) xg::XGPath::load (C++ function) xg::XGPath::mapping (C++ function) xg::XGPath::nodes (C++ member) xg::XGPath::nodes_rank (C++ member) xg::XGPath::nodes_select (C++ member) xg::XGPath::offsets (C++ member) xg::XGPath::offsets_rank (C++ member) xg::XGPath::offsets_select (C++ member) xg::XGPath::operator= (C++ function), [1] xg::XGPath::positions (C++ member) xg::XGPath::ranks (C++ member) xg::XGPath::serialize (C++ function) xg::XGPath::XGPath (C++ function), [1], [2], [3] xg::XGPath::~XGPath (C++ function)