Index

A

append() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method) append_step() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutablePathHandleGraph method) apply_ordering() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutableHandleGraph method) apply_orientation() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutableHandleGraph method) assign() (bdsg.bdsg.HashGraph method) (bdsg.bdsg.PackedGraph method) (bdsg.handlegraph.DeletableHandleGraph method) (bdsg.handlegraph.ExpandingOverlayGraph method) (bdsg.handlegraph.handle_t method) (bdsg.handlegraph.HandleGraph method) (bdsg.handlegraph.MutableHandleGraph method) (bdsg.handlegraph.MutablePathDeletableHandleGraph method) (bdsg.handlegraph.MutablePathHandleGraph method) (bdsg.handlegraph.MutablePathMutableHandleGraph method) (bdsg.handlegraph.path_handle_t method) (bdsg.handlegraph.PathHandleGraph method) (bdsg.handlegraph.PathPositionHandleGraph method) (bdsg.handlegraph.RankedHandleGraph method) (bdsg.handlegraph.SerializableHandleGraph method) (bdsg.handlegraph.SnarlDecomposition method) (bdsg.handlegraph.step_handle_t method) (bdsg.handlegraph.VectorizableHandleGraph method)

B

bdsg.bdsg module bdsg.handlegraph module bdsg.std module bdsg::HashGraph (C++ class) bdsg::HashGraph::append_step (C++ function) bdsg::HashGraph::apply_ordering (C++ function) bdsg::HashGraph::apply_orientation (C++ function) bdsg::HashGraph::change_sequence (C++ function) bdsg::HashGraph::clear (C++ function) bdsg::HashGraph::create_edge (C++ function) bdsg::HashGraph::create_handle (C++ function), [1] bdsg::HashGraph::create_path_handle (C++ function) bdsg::HashGraph::destroy_edge (C++ function) bdsg::HashGraph::destroy_handle (C++ function) bdsg::HashGraph::destroy_path (C++ function) bdsg::HashGraph::destroy_paths (C++ function) bdsg::HashGraph::divide_handle (C++ function) bdsg::HashGraph::flip (C++ function) bdsg::HashGraph::follow_edges_impl (C++ function) bdsg::HashGraph::for_each_handle_impl (C++ function) bdsg::HashGraph::for_each_path_handle_impl (C++ function) bdsg::HashGraph::for_each_step_on_handle_impl (C++ function) bdsg::HashGraph::get_base (C++ function) bdsg::HashGraph::get_degree (C++ function) bdsg::HashGraph::get_handle (C++ function) bdsg::HashGraph::get_handle_of_step (C++ function) bdsg::HashGraph::get_id (C++ function) bdsg::HashGraph::get_is_circular (C++ function) bdsg::HashGraph::get_is_reverse (C++ function) bdsg::HashGraph::get_length (C++ function) bdsg::HashGraph::get_magic_number (C++ function) bdsg::HashGraph::get_next_step (C++ function) bdsg::HashGraph::get_node_count (C++ function) bdsg::HashGraph::get_path_count (C++ function) bdsg::HashGraph::get_path_handle (C++ function) bdsg::HashGraph::get_path_handle_of_step (C++ function) bdsg::HashGraph::get_path_name (C++ function) bdsg::HashGraph::get_previous_step (C++ function) bdsg::HashGraph::get_sequence (C++ function) bdsg::HashGraph::get_step_count (C++ function) bdsg::HashGraph::get_subsequence (C++ function) bdsg::HashGraph::has_next_step (C++ function) bdsg::HashGraph::has_node (C++ function) bdsg::HashGraph::has_path (C++ function) bdsg::HashGraph::has_previous_step (C++ function) bdsg::HashGraph::HashGraph (C++ function), [1] bdsg::HashGraph::increment_node_ids (C++ function) bdsg::HashGraph::max_node_id (C++ function) bdsg::HashGraph::min_node_id (C++ function) bdsg::HashGraph::optimize (C++ function) bdsg::HashGraph::path_back (C++ function) bdsg::HashGraph::path_begin (C++ function) bdsg::HashGraph::path_end (C++ function) bdsg::HashGraph::path_front_end (C++ function) bdsg::HashGraph::prepend_step (C++ function) bdsg::HashGraph::reassign_node_ids (C++ function) bdsg::HashGraph::rewrite_segment (C++ function) bdsg::HashGraph::set_circularity (C++ function) bdsg::HashGraph::set_id_increment (C++ function) bdsg::HashGraph::truncate_handle (C++ function) bdsg::MutablePositionOverlay (C++ class) bdsg::OverlayHelper (C++ class) bdsg::OverlayHelper::apply (C++ function), [1] bdsg::OverlayHelper::get (C++ function) bdsg::PackedGraph (C++ class) bdsg::PackedPositionOverlay (C++ class) bdsg::PairOverlayHelper (C++ class) bdsg::PairOverlayHelper::apply (C++ function), [1] bdsg::PairOverlayHelper::get (C++ function) bdsg::PathPositionOverlayHelper (C++ type) bdsg::PathPositionVectorizableOverlay (C++ class) bdsg::PathPositionVectorizableOverlayHelper (C++ type) bdsg::PathRankedOverlayHelper (C++ type) bdsg::PathVectorizableOverlay (C++ class) bdsg::PathVectorizableOverlayHelper (C++ type) bdsg::PositionOverlay (C++ class) bdsg::RankedOverlayHelper (C++ type) bdsg::SnarlDistanceIndex (C++ class) bdsg::SnarlDistanceIndex::canonical (C++ function) bdsg::SnarlDistanceIndex::chain_minimum_length (C++ function) bdsg::SnarlDistanceIndex::check_version_on_load (C++ function) bdsg::SnarlDistanceIndex::connected_component_count (C++ function) bdsg::SnarlDistanceIndex::connectivity_t (C++ enum) bdsg::SnarlDistanceIndex::connectivity_t::END_END (C++ enumerator) bdsg::SnarlDistanceIndex::connectivity_t::END_START (C++ enumerator) bdsg::SnarlDistanceIndex::connectivity_t::END_TIP (C++ enumerator) bdsg::SnarlDistanceIndex::connectivity_t::START_END (C++ enumerator) bdsg::SnarlDistanceIndex::connectivity_t::START_START (C++ enumerator) bdsg::SnarlDistanceIndex::connectivity_t::START_TIP (C++ enumerator) bdsg::SnarlDistanceIndex::connectivity_t::TIP_END (C++ enumerator)

bdsg::SnarlDistanceIndex::connectivity_t::TIP_START (C++ enumerator) bdsg::SnarlDistanceIndex::connectivity_t::TIP_TIP (C++ enumerator) bdsg::SnarlDistanceIndex::deserialize (C++ function), [1], [2], [3] bdsg::SnarlDistanceIndex::deserialize_members (C++ function) bdsg::SnarlDistanceIndex::dissociate (C++ function) bdsg::SnarlDistanceIndex::distance_to_parent_bound (C++ function) bdsg::SnarlDistanceIndex::ends_at (C++ function) bdsg::SnarlDistanceIndex::flip (C++ function) bdsg::SnarlDistanceIndex::get_bound (C++ function) bdsg::SnarlDistanceIndex::get_depth (C++ function) bdsg::SnarlDistanceIndex::get_forward_loop_value (C++ function) bdsg::SnarlDistanceIndex::get_handle (C++ function) bdsg::SnarlDistanceIndex::get_handle_from_connected_component (C++ function) bdsg::SnarlDistanceIndex::get_magic_number (C++ function) bdsg::SnarlDistanceIndex::get_max_prefix_sum_value (C++ function) bdsg::SnarlDistanceIndex::get_max_tree_depth (C++ function) bdsg::SnarlDistanceIndex::get_net (C++ function) bdsg::SnarlDistanceIndex::get_node_from_sentinel (C++ function) bdsg::SnarlDistanceIndex::get_node_net_handle (C++ function) bdsg::SnarlDistanceIndex::get_node_pointer_offset (C++ function) bdsg::SnarlDistanceIndex::get_node_record_offset (C++ function) bdsg::SnarlDistanceIndex::get_parent (C++ function) bdsg::SnarlDistanceIndex::get_parent_traversal (C++ function) bdsg::SnarlDistanceIndex::get_prefix_sum_value (C++ function) bdsg::SnarlDistanceIndex::get_rank_in_parent (C++ function) bdsg::SnarlDistanceIndex::get_record_handle_type (C++ function) bdsg::SnarlDistanceIndex::get_record_offset (C++ function) bdsg::SnarlDistanceIndex::get_reverse_loop_value (C++ function) bdsg::SnarlDistanceIndex::get_root (C++ function) bdsg::SnarlDistanceIndex::get_snarl_child_from_rank (C++ function) bdsg::SnarlDistanceIndex::has_connectivity (C++ function) bdsg::SnarlDistanceIndex::has_distances (C++ function), [1] bdsg::SnarlDistanceIndex::has_external_connectivity (C++ function) bdsg::SnarlDistanceIndex::has_node (C++ function) bdsg::SnarlDistanceIndex::into_which_snarl (C++ function) bdsg::SnarlDistanceIndex::is_chain (C++ function) bdsg::SnarlDistanceIndex::is_dag (C++ function) bdsg::SnarlDistanceIndex::is_looping_chain (C++ function) bdsg::SnarlDistanceIndex::is_multicomponent_chain (C++ function) bdsg::SnarlDistanceIndex::is_node (C++ function) bdsg::SnarlDistanceIndex::is_ordered_in_chain (C++ function) bdsg::SnarlDistanceIndex::is_oversized_snarl (C++ function) bdsg::SnarlDistanceIndex::is_regular_snarl (C++ function) bdsg::SnarlDistanceIndex::is_reversed_in_parent (C++ function) bdsg::SnarlDistanceIndex::is_root (C++ function) bdsg::SnarlDistanceIndex::is_root_snarl (C++ function) bdsg::SnarlDistanceIndex::is_sentinel (C++ function) bdsg::SnarlDistanceIndex::is_simple_snarl (C++ function) bdsg::SnarlDistanceIndex::is_snarl (C++ function) bdsg::SnarlDistanceIndex::is_trivial_chain (C++ function) bdsg::SnarlDistanceIndex::lowest_common_ancestor (C++ function) bdsg::SnarlDistanceIndex::max_distance_in_parent (C++ function) bdsg::SnarlDistanceIndex::maximum_distance (C++ function) bdsg::SnarlDistanceIndex::minimum_distance (C++ function) bdsg::SnarlDistanceIndex::minimum_length (C++ function) bdsg::SnarlDistanceIndex::net_handle_record_t (C++ enum) bdsg::SnarlDistanceIndex::net_handle_record_t::CHAIN_HANDLE (C++ enumerator) bdsg::SnarlDistanceIndex::net_handle_record_t::NODE_HANDLE (C++ enumerator) bdsg::SnarlDistanceIndex::net_handle_record_t::ROOT_HANDLE (C++ enumerator) bdsg::SnarlDistanceIndex::net_handle_record_t::SENTINEL_HANDLE (C++ enumerator) bdsg::SnarlDistanceIndex::net_handle_record_t::SNARL_HANDLE (C++ enumerator) bdsg::SnarlDistanceIndex::node_id (C++ function) bdsg::SnarlDistanceIndex::node_length (C++ function) bdsg::SnarlDistanceIndex::preload (C++ function) bdsg::SnarlDistanceIndex::record_t (C++ enum) bdsg::SnarlDistanceIndex::record_t::CHAIN (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::CHILDREN (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::DISTANCED_CHAIN (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::DISTANCED_NODE (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::DISTANCED_ROOT_SNARL (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::DISTANCED_SIMPLE_SNARL (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::DISTANCED_SNARL (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::DISTANCED_TRIVIAL_SNARL (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::MULTICOMPONENT_CHAIN (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::NODE (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::OVERSIZED_SNARL (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::ROOT (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::ROOT_SNARL (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::SIMPLE_SNARL (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::SNARL (C++ enumerator) bdsg::SnarlDistanceIndex::record_t::TRIVIAL_SNARL (C++ enumerator) bdsg::SnarlDistanceIndex::serialize (C++ function), [1], [2], [3], [4], [5], [6], [7], [8] bdsg::SnarlDistanceIndex::serialize_members (C++ function) bdsg::SnarlDistanceIndex::start_end_traversal_of (C++ function) bdsg::SnarlDistanceIndex::starts_at (C++ function) bdsg::SnarlDistanceIndex::sum (C++ function) bdsg::SnarlDistanceIndex::TemporaryDistanceIndex (C++ class) bdsg::SnarlDistanceIndex::TemporaryDistanceIndex::TemporaryChainRecord (C++ struct) bdsg::SnarlDistanceIndex::TemporaryDistanceIndex::TemporaryNodeRecord (C++ struct) bdsg::SnarlDistanceIndex::TemporaryDistanceIndex::TemporaryRecord (C++ struct) bdsg::SnarlDistanceIndex::TemporaryDistanceIndex::TemporarySnarlRecord (C++ struct) bdsg::VectorizableOverlay (C++ class) bdsg::VectorizableOverlayHelper (C++ type) bit_width() (bdsg.bdsg.SnarlDistanceIndex static method)

C

canonical() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) capacity() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method) chain_minimum_length() (bdsg.bdsg.SnarlDistanceIndex method) change_sequence() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.DeletableHandleGraph method) (bdsg.handlegraph.MutablePathDeletableHandleGraph method) clear() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.DeletableHandleGraph method) (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method)

connected_component_count() (bdsg.bdsg.SnarlDistanceIndex method) connectivity_to_endpoints() (bdsg.bdsg.SnarlDistanceIndex static method) count() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method) create_edge() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutableHandleGraph method) create_handle() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutableHandleGraph method) create_path_handle() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutablePathHandleGraph method)

D

DeletableHandleGraph (class in bdsg.handlegraph) deserialize() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SerializableHandleGraph method) destroy_edge() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.DeletableHandleGraph method) destroy_handle() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.DeletableHandleGraph method) destroy_path() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutablePathHandleGraph method)

destroy_paths() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutablePathHandleGraph method) dissociate() (bdsg.bdsg.SnarlDistanceIndex method) distance_in_parent() (bdsg.bdsg.SnarlDistanceIndex method) distance_in_snarl() (bdsg.bdsg.SnarlDistanceIndex method) distance_to_parent_bound() (bdsg.bdsg.SnarlDistanceIndex method) divide_handle() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutableHandleGraph method)

E

edge_handle() (bdsg.handlegraph.HandleGraph method) edge_index() (bdsg.handlegraph.VectorizableHandleGraph method) empty() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method) endpoints_to_connectivity() (bdsg.bdsg.SnarlDistanceIndex static method) ends_at() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method)

ends_at_end() (bdsg.handlegraph.SnarlDecomposition method) ends_at_start() (bdsg.handlegraph.SnarlDecomposition method) ends_at_tip() (bdsg.handlegraph.SnarlDecomposition method) ExpandingOverlayGraph (class in bdsg.handlegraph) extend() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method)

F

flip() (bdsg.bdsg.HashGraph method) (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.HandleGraph method) (bdsg.handlegraph.SnarlDecomposition method) follow_edges() (bdsg.handlegraph.HandleGraph method) follow_edges_impl() (bdsg.bdsg.HashGraph method) follow_net_edges() (bdsg.handlegraph.SnarlDecomposition method) for_each_child() (bdsg.handlegraph.SnarlDecomposition method) for_each_edge() (bdsg.handlegraph.HandleGraph method) for_each_handle() (bdsg.handlegraph.HandleGraph method) for_each_handle_impl() (bdsg.bdsg.HashGraph method)

for_each_path_handle() (bdsg.handlegraph.PathHandleGraph method) for_each_path_handle_impl() (bdsg.bdsg.HashGraph method) for_each_step_in_path() (bdsg.handlegraph.PathHandleGraph method) for_each_step_on_handle() (bdsg.handlegraph.PathHandleGraph method) for_each_step_on_handle_impl() (bdsg.bdsg.HashGraph method) for_each_step_position_on_handle() (bdsg.handlegraph.PathPositionHandleGraph method) for_each_tippy_child() (bdsg.handlegraph.SnarlDecomposition method) for_each_traversal() (bdsg.handlegraph.SnarlDecomposition method) for_each_traversal_end() (bdsg.handlegraph.SnarlDecomposition method) for_each_traversal_start() (bdsg.handlegraph.SnarlDecomposition method) forward() (bdsg.handlegraph.HandleGraph method)

G

get_base() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.HandleGraph method) get_bound() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) get_chain_component() (bdsg.bdsg.SnarlDistanceIndex method) get_connected_component_number() (bdsg.bdsg.SnarlDistanceIndex method) get_connectivity() (bdsg.bdsg.SnarlDistanceIndex static method) get_degree() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.HandleGraph method) get_depth() (bdsg.bdsg.SnarlDistanceIndex method) get_edge_count() (bdsg.handlegraph.HandleGraph method) get_end_bound() (bdsg.handlegraph.SnarlDecomposition method) get_end_endpoint() (bdsg.bdsg.SnarlDistanceIndex static method) get_forward_loop_value() (bdsg.bdsg.SnarlDistanceIndex method) get_handle() (bdsg.bdsg.HashGraph method) (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.HandleGraph method) (bdsg.handlegraph.SnarlDecomposition method) get_handle_from_connected_component() (bdsg.bdsg.SnarlDistanceIndex method) get_handle_of_step() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) get_handle_type() (bdsg.bdsg.SnarlDistanceIndex static method) get_id() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.HandleGraph method) get_is_circular() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) get_is_reverse() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.HandleGraph method) get_length() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.HandleGraph method) get_magic_number() (bdsg.bdsg.HashGraph method) (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SerializableHandleGraph method) get_max_prefix_sum_value() (bdsg.bdsg.SnarlDistanceIndex method) get_max_tree_depth() (bdsg.bdsg.SnarlDistanceIndex method) get_net() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) get_net_handle() (bdsg.bdsg.SnarlDistanceIndex method) get_net_handle_from_values() (bdsg.bdsg.SnarlDistanceIndex static method) get_next_step() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) get_node_count() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.HandleGraph method)

get_node_from_sentinel() (bdsg.bdsg.SnarlDistanceIndex method) get_node_net_handle() (bdsg.bdsg.SnarlDistanceIndex method) get_node_pointer_offset() (bdsg.bdsg.SnarlDistanceIndex static method) get_node_record_offset() (bdsg.bdsg.SnarlDistanceIndex static method) get_parent() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) get_parent_traversal() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) get_path_count() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) get_path_handle() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) get_path_handle_of_step() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) get_path_length() (bdsg.handlegraph.PathPositionHandleGraph method) get_path_name() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) get_position_of_step() (bdsg.handlegraph.PathPositionHandleGraph method) get_prefix() (bdsg.bdsg.SnarlDistanceIndex method) get_prefix_sum_value() (bdsg.bdsg.SnarlDistanceIndex method) get_previous_step() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) get_rank_in_parent() (bdsg.bdsg.SnarlDistanceIndex method) get_record_handle_type() (bdsg.bdsg.SnarlDistanceIndex static method) get_record_offset() (bdsg.bdsg.SnarlDistanceIndex static method) get_reverse_loop_value() (bdsg.bdsg.SnarlDistanceIndex method) get_root() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) get_sequence() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.HandleGraph method) get_snarl_child_from_rank() (bdsg.bdsg.SnarlDistanceIndex method) get_start_bound() (bdsg.handlegraph.SnarlDecomposition method) get_start_endpoint() (bdsg.bdsg.SnarlDistanceIndex static method) get_step_at_position() (bdsg.handlegraph.PathPositionHandleGraph method) get_step_count() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) get_subsequence() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.HandleGraph method) get_total_length() (bdsg.handlegraph.HandleGraph method) get_underlying_handle() (bdsg.handlegraph.ExpandingOverlayGraph method) get_usage() (bdsg.bdsg.SnarlDistanceIndex method)

H

handle_t (class in bdsg.handlegraph) handle_to_rank() (bdsg.handlegraph.RankedHandleGraph method) HandleGraph (class in bdsg.handlegraph) handlegraph::DeletableHandleGraph (C++ class) handlegraph::DeletableHandleGraph::change_sequence (C++ function) handlegraph::DeletableHandleGraph::clear (C++ function) handlegraph::DeletableHandleGraph::destroy_edge (C++ function), [1] handlegraph::DeletableHandleGraph::destroy_handle (C++ function) handlegraph::DeletableHandleGraph::truncate_handle (C++ function) handlegraph::ExpandingOverlayGraph (C++ class) handlegraph::ExpandingOverlayGraph::get_underlying_handle (C++ function) handlegraph::ExpandingOverlayGraph::~ExpandingOverlayGraph (C++ function) handlegraph::handle_t (C++ struct) handlegraph::HandleGraph (C++ class) handlegraph::HandleGraph::edge_handle (C++ function) handlegraph::HandleGraph::flip (C++ function) handlegraph::HandleGraph::follow_edges (C++ function) handlegraph::HandleGraph::for_each_edge (C++ function) handlegraph::HandleGraph::for_each_handle (C++ function) handlegraph::HandleGraph::forward (C++ function) handlegraph::HandleGraph::get_base (C++ function) handlegraph::HandleGraph::get_degree (C++ function) handlegraph::HandleGraph::get_edge_count (C++ function) handlegraph::HandleGraph::get_handle (C++ function) handlegraph::HandleGraph::get_id (C++ function) handlegraph::HandleGraph::get_is_reverse (C++ function) handlegraph::HandleGraph::get_length (C++ function) handlegraph::HandleGraph::get_node_count (C++ function) handlegraph::HandleGraph::get_sequence (C++ function) handlegraph::HandleGraph::get_subsequence (C++ function) handlegraph::HandleGraph::get_total_length (C++ function) handlegraph::HandleGraph::has_edge (C++ function), [1] handlegraph::HandleGraph::has_node (C++ function) handlegraph::HandleGraph::max_node_id (C++ function) handlegraph::HandleGraph::min_node_id (C++ function) handlegraph::HandleGraph::traverse_edge_handle (C++ function) handlegraph::MutableHandleGraph (C++ class) handlegraph::MutableHandleGraph::apply_ordering (C++ function) handlegraph::MutableHandleGraph::apply_orientation (C++ function) handlegraph::MutableHandleGraph::create_edge (C++ function), [1] handlegraph::MutableHandleGraph::create_handle (C++ function), [1] handlegraph::MutableHandleGraph::divide_handle (C++ function), [1] handlegraph::MutableHandleGraph::increment_node_ids (C++ function), [1] handlegraph::MutableHandleGraph::optimize (C++ function) handlegraph::MutableHandleGraph::reassign_node_ids (C++ function) handlegraph::MutableHandleGraph::set_id_increment (C++ function) handlegraph::MutablePathDeletableHandleGraph (C++ class) handlegraph::MutablePathDeletableHandleGraph::change_sequence (C++ function) handlegraph::MutablePathHandleGraph (C++ class) handlegraph::MutablePathHandleGraph::append_step (C++ function) handlegraph::MutablePathHandleGraph::create_path_handle (C++ function) handlegraph::MutablePathHandleGraph::destroy_path (C++ function) handlegraph::MutablePathHandleGraph::destroy_paths (C++ function) handlegraph::MutablePathHandleGraph::pop_back_step (C++ function) handlegraph::MutablePathHandleGraph::pop_front_step (C++ function) handlegraph::MutablePathHandleGraph::prepend_step (C++ function) handlegraph::MutablePathHandleGraph::rename_path (C++ function) handlegraph::MutablePathHandleGraph::rewrite_segment (C++ function) handlegraph::MutablePathHandleGraph::set_circularity (C++ function) handlegraph::MutablePathMutableHandleGraph (C++ class) handlegraph::net_handle_t (C++ struct) handlegraph::path_handle_t (C++ struct) handlegraph::PathHandleGraph (C++ class) handlegraph::PathHandleGraph::for_each_path_handle (C++ function) handlegraph::PathHandleGraph::for_each_step_in_path (C++ function) handlegraph::PathHandleGraph::for_each_step_on_handle (C++ function) handlegraph::PathHandleGraph::get_handle_of_step (C++ function) handlegraph::PathHandleGraph::get_is_circular (C++ function) handlegraph::PathHandleGraph::get_next_step (C++ function) handlegraph::PathHandleGraph::get_path_count (C++ function) handlegraph::PathHandleGraph::get_path_handle (C++ function) handlegraph::PathHandleGraph::get_path_handle_of_step (C++ function) handlegraph::PathHandleGraph::get_path_name (C++ function) handlegraph::PathHandleGraph::get_previous_step (C++ function)

handlegraph::PathHandleGraph::get_step_count (C++ function), [1] handlegraph::PathHandleGraph::has_next_step (C++ function) handlegraph::PathHandleGraph::has_path (C++ function) handlegraph::PathHandleGraph::has_previous_step (C++ function) handlegraph::PathHandleGraph::is_empty (C++ function) handlegraph::PathHandleGraph::path_back (C++ function) handlegraph::PathHandleGraph::path_begin (C++ function) handlegraph::PathHandleGraph::path_end (C++ function) handlegraph::PathHandleGraph::path_front_end (C++ function) handlegraph::PathHandleGraph::scan_path (C++ function) handlegraph::PathHandleGraph::steps_of_handle (C++ function) handlegraph::PathPositionHandleGraph (C++ class) handlegraph::PathPositionHandleGraph::for_each_step_position_on_handle (C++ function) handlegraph::PathPositionHandleGraph::get_path_length (C++ function) handlegraph::PathPositionHandleGraph::get_position_of_step (C++ function) handlegraph::PathPositionHandleGraph::get_step_at_position (C++ function) handlegraph::RankedHandleGraph (C++ class) handlegraph::RankedHandleGraph::handle_to_rank (C++ function) handlegraph::RankedHandleGraph::id_to_rank (C++ function) handlegraph::RankedHandleGraph::rank_to_handle (C++ function) handlegraph::RankedHandleGraph::rank_to_id (C++ function) handlegraph::SerializableHandleGraph (C++ class) handlegraph::SnarlDecomposition (C++ class) handlegraph::SnarlDecomposition::canonical (C++ function) handlegraph::SnarlDecomposition::endpoint_t (C++ enum) handlegraph::SnarlDecomposition::endpoint_t::END (C++ enumerator) handlegraph::SnarlDecomposition::endpoint_t::START (C++ enumerator) handlegraph::SnarlDecomposition::endpoint_t::TIP (C++ enumerator) handlegraph::SnarlDecomposition::ends_at (C++ function) handlegraph::SnarlDecomposition::ends_at_end (C++ function) handlegraph::SnarlDecomposition::ends_at_start (C++ function) handlegraph::SnarlDecomposition::ends_at_tip (C++ function) handlegraph::SnarlDecomposition::flip (C++ function) handlegraph::SnarlDecomposition::follow_net_edges (C++ function) handlegraph::SnarlDecomposition::for_each_child (C++ function) handlegraph::SnarlDecomposition::for_each_tippy_child (C++ function) handlegraph::SnarlDecomposition::for_each_traversal (C++ function) handlegraph::SnarlDecomposition::for_each_traversal_end (C++ function) handlegraph::SnarlDecomposition::for_each_traversal_start (C++ function) handlegraph::SnarlDecomposition::get_bound (C++ function) handlegraph::SnarlDecomposition::get_end_bound (C++ function) handlegraph::SnarlDecomposition::get_handle (C++ function) handlegraph::SnarlDecomposition::get_net (C++ function) handlegraph::SnarlDecomposition::get_parent (C++ function) handlegraph::SnarlDecomposition::get_parent_traversal (C++ function) handlegraph::SnarlDecomposition::get_root (C++ function) handlegraph::SnarlDecomposition::get_start_bound (C++ function) handlegraph::SnarlDecomposition::is_chain (C++ function) handlegraph::SnarlDecomposition::is_node (C++ function) handlegraph::SnarlDecomposition::is_root (C++ function) handlegraph::SnarlDecomposition::is_sentinel (C++ function) handlegraph::SnarlDecomposition::is_snarl (C++ function) handlegraph::SnarlDecomposition::starts_at (C++ function) handlegraph::SnarlDecomposition::starts_at_end (C++ function) handlegraph::SnarlDecomposition::starts_at_start (C++ function) handlegraph::SnarlDecomposition::starts_at_tip (C++ function) handlegraph::step_handle_t (C++ struct) handlegraph::VectorizableHandleGraph (C++ class) handlegraph::VectorizableHandleGraph::edge_index (C++ function) handlegraph::VectorizableHandleGraph::node_at_vector_offset (C++ function) handlegraph::VectorizableHandleGraph::node_vector_offset (C++ function) has_connectivity() (bdsg.bdsg.SnarlDistanceIndex method) has_distances() (bdsg.bdsg.SnarlDistanceIndex static method) has_edge() (bdsg.handlegraph.HandleGraph method) has_external_connectivity() (bdsg.bdsg.SnarlDistanceIndex method) has_next_step() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) has_node() (bdsg.bdsg.HashGraph method) (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.HandleGraph method) has_path() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) has_previous_step() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) HashGraph (class in bdsg.bdsg)

I

id_to_rank() (bdsg.handlegraph.RankedHandleGraph method) increment_node_ids() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutableHandleGraph method) insert() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method) into_which_snarl() (bdsg.bdsg.SnarlDistanceIndex method) is_chain() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) is_dag() (bdsg.bdsg.SnarlDistanceIndex method) is_empty() (bdsg.handlegraph.PathHandleGraph method) is_externally_end_end_connected() (bdsg.bdsg.SnarlDistanceIndex method) is_externally_start_end_connected() (bdsg.bdsg.SnarlDistanceIndex method) is_externally_start_start_connected() (bdsg.bdsg.SnarlDistanceIndex method) is_looping_chain() (bdsg.bdsg.SnarlDistanceIndex method)

is_multicomponent_chain() (bdsg.bdsg.SnarlDistanceIndex method) is_node() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) is_ordered_in_chain() (bdsg.bdsg.SnarlDistanceIndex method) is_regular_snarl() (bdsg.bdsg.SnarlDistanceIndex method) is_reversed_in_parent() (bdsg.bdsg.SnarlDistanceIndex method) is_root() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) is_root_snarl() (bdsg.bdsg.SnarlDistanceIndex method) is_sentinel() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) is_simple_snarl() (bdsg.bdsg.SnarlDistanceIndex method) is_snarl() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) is_trivial_chain() (bdsg.bdsg.SnarlDistanceIndex method)

L

lowest_common_ancestor() (bdsg.bdsg.SnarlDistanceIndex method)

M

max_distance_in_parent() (bdsg.bdsg.SnarlDistanceIndex method) max_node_id() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.HandleGraph method) max_size() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method) maximum() (bdsg.bdsg.SnarlDistanceIndex static method) maximum_distance() (bdsg.bdsg.SnarlDistanceIndex method) maximum_length() (bdsg.bdsg.SnarlDistanceIndex method) min_node_id() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.HandleGraph method)

minimum_length() (bdsg.bdsg.SnarlDistanceIndex method) minus() (bdsg.bdsg.SnarlDistanceIndex static method) module bdsg.bdsg bdsg.handlegraph bdsg.std MutableHandleGraph (class in bdsg.handlegraph) MutablePathDeletableHandleGraph (class in bdsg.handlegraph) MutablePathHandleGraph (class in bdsg.handlegraph) MutablePathMutableHandleGraph (class in bdsg.handlegraph) MutablePositionOverlay (class in bdsg.bdsg)

N

name (bdsg.bdsg.SnarlDistanceIndex.connectivity_t property) (bdsg.bdsg.SnarlDistanceIndex.net_handle_record_t property) (bdsg.bdsg.SnarlDistanceIndex.record_t property) (bdsg.bdsg.SnarlDistanceIndex.temp_record_t property) (bdsg.handlegraph.SnarlDecomposition.endpoint_t property)

net_handle_as_string() (bdsg.bdsg.SnarlDistanceIndex method) net_handle_t (class in bdsg.handlegraph) node_at_vector_offset() (bdsg.handlegraph.VectorizableHandleGraph method) node_id() (bdsg.bdsg.SnarlDistanceIndex method) node_length() (bdsg.bdsg.SnarlDistanceIndex method) node_vector_offset() (bdsg.handlegraph.VectorizableHandleGraph method)

O

optimize() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutableHandleGraph method)

P

PackedGraph (class in bdsg.bdsg) PackedPositionOverlay (class in bdsg.bdsg) path_back() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) path_begin() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) path_end() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) path_front_end() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.PathHandleGraph method) path_handle_t (class in bdsg.handlegraph) PathHandleGraph (class in bdsg.handlegraph) PathPositionHandleGraph (class in bdsg.handlegraph)

PathPositionVectorizableOverlay (class in bdsg.bdsg) PathVectorizableOverlay (class in bdsg.bdsg) pop() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method) pop_back_step() (bdsg.handlegraph.MutablePathHandleGraph method) pop_front_step() (bdsg.handlegraph.MutablePathHandleGraph method) PositionOverlay (class in bdsg.bdsg) preload() (bdsg.bdsg.SnarlDistanceIndex method) prepend_step() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutablePathHandleGraph method) print_descendants_of() (bdsg.bdsg.SnarlDistanceIndex method) print_self() (bdsg.bdsg.SnarlDistanceIndex method) print_snarl_stats() (bdsg.bdsg.SnarlDistanceIndex method)

R

rank_to_handle() (bdsg.handlegraph.RankedHandleGraph method) rank_to_id() (bdsg.handlegraph.RankedHandleGraph method) RankedHandleGraph (class in bdsg.handlegraph) reassign_node_ids() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutableHandleGraph method) remove() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method)

rename_path() (bdsg.handlegraph.MutablePathHandleGraph method) reserve() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method) rewrite_segment() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutablePathHandleGraph method)

S

scan_path() (bdsg.handlegraph.PathHandleGraph method) SerializableHandleGraph (class in bdsg.handlegraph) serialize() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SerializableHandleGraph method) set_circularity() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutablePathHandleGraph method) set_id_increment() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.MutableHandleGraph method) set_only_top_level_chain_distances() (bdsg.bdsg.SnarlDistanceIndex method) set_snarl_size_limit() (bdsg.bdsg.SnarlDistanceIndex method) shrink_to_fit() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method) SnarlDecomposition (class in bdsg.handlegraph) SnarlDecomposition.endpoint_t (class in bdsg.handlegraph) SnarlDistanceIndex (class in bdsg.bdsg)

SnarlDistanceIndex.connectivity_t (class in bdsg.bdsg) SnarlDistanceIndex.net_handle_record_t (class in bdsg.bdsg) SnarlDistanceIndex.record_t (class in bdsg.bdsg) SnarlDistanceIndex.temp_record_t (class in bdsg.bdsg) start_end_traversal_of() (bdsg.bdsg.SnarlDistanceIndex method) starts_at() (bdsg.bdsg.SnarlDistanceIndex method) (bdsg.handlegraph.SnarlDecomposition method) starts_at_end() (bdsg.handlegraph.SnarlDecomposition method) starts_at_start() (bdsg.handlegraph.SnarlDecomposition method) starts_at_tip() (bdsg.handlegraph.SnarlDecomposition method) step_handle_t (class in bdsg.handlegraph) steps_of_handle() (bdsg.handlegraph.PathHandleGraph method) sum() (bdsg.bdsg.SnarlDistanceIndex static method) swap() (bdsg.std.vector_handlegraph_handle_t method) (bdsg.std.vector_handlegraph_step_handle_t method) (bdsg.std.vector_unsigned_long method)

T

time_accesses() (bdsg.bdsg.SnarlDistanceIndex method) traverse_decomposition() (bdsg.bdsg.SnarlDistanceIndex method) traverse_decomposition_helper() (bdsg.bdsg.SnarlDistanceIndex method)

traverse_edge_handle() (bdsg.handlegraph.HandleGraph method) truncate_handle() (bdsg.bdsg.HashGraph method) (bdsg.handlegraph.DeletableHandleGraph method)

V

validate_ancestors_of() (bdsg.bdsg.SnarlDistanceIndex method) validate_descendants_of() (bdsg.bdsg.SnarlDistanceIndex method) validate_index() (bdsg.bdsg.SnarlDistanceIndex method) vector_handlegraph_handle_t (class in bdsg.std)

vector_handlegraph_step_handle_t (class in bdsg.std) vector_unsigned_long (class in bdsg.std) VectorizableHandleGraph (class in bdsg.handlegraph) VectorizableOverlay (class in bdsg.bdsg)

W

write_snarls_to_json() (bdsg.bdsg.SnarlDistanceIndex method)