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C++ API
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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V
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W
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::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::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::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)
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_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::has_connectivity (C++ function)
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_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_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]
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)
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)
dissociate() (bdsg.bdsg.SnarlDistanceIndex method)
distance_in_parent() (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_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_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::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::MutablePathHandleGraph (C++ class)
handlegraph::MutablePathHandleGraph::append_step (C++ function)
handlegraph::MutablePathHandleGraph::create_path_handle (C++ function)
handlegraph::MutablePathHandleGraph::destroy_path (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_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_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_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_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)
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