#include "clip.hpp"
#include "traversal_finder.hpp"
#include <unordered_map>
#include <IntervalTree.h>
#include <structures/rank_pairing_heap.hpp>
#include <BooPHF.h>
#include "bdsg/internal/hash_map.hpp"
#include "bdsg/internal/packed_structs.hpp"

Classes
struct	vg::BBEdgeHash

Namespaces
	vg

Functions
void	vg::visit_contained_snarls (const PathPositionHandleGraph graph, const vector< Region > &regions, SnarlManager &snarl_manager, bool include_endpoints, function< void(const Snarl , step_handle_t, step_handle_t, int64_t, int64_t, bool, const Region *)> visit_fn)

void	vg::delete_nodes_and_chop_paths (MutablePathMutableHandleGraph graph, const unordered_set< nid_t > &nodes_to_delete, const unordered_set< edge_t > &edges_to_delete, int64_t min_fragment_len, unordered_map< string, size_t > fragments_per_path)

void	vg::clip_contained_snarls (MutablePathMutableHandleGraph graph, PathPositionHandleGraph pp_graph, const vector< Region > &regions, SnarlManager &snarl_manager, bool include_endpoints, int64_t min_fragment_len, size_t max_nodes, size_t max_edges, size_t max_nodes_shallow, size_t max_edges_shallow, double max_avg_degree, double max_reflen_prop, size_t max_reflen, bool out_bed, bool verbose)

void	vg::clip_low_depth_nodes_and_edges_generic (MutablePathMutableHandleGraph graph, function< void(function< void(handle_t, const Region )>)> iterate_handles, function< void(function< void(edge_t, const Region *)>)> iterate_edges, int64_t min_depth, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

void	vg::clip_low_depth_nodes_and_edges (MutablePathMutableHandleGraph *graph, int64_t min_depth, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

void	vg::clip_contained_low_depth_nodes_and_edges (MutablePathMutableHandleGraph graph, PathPositionHandleGraph pp_graph, const vector< Region > &regions, SnarlManager &snarl_manager, bool include_endpoints, int64_t min_depth, int64_t min_fragment_len, bool verbose)

void	vg::clip_deletion_edges (MutablePathMutableHandleGraph *graph, int64_t max_deletion, int64_t context_steps, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

void	vg::clip_stubs_generic (MutablePathMutableHandleGraph graph, function< void(function< void(handle_t, const Region )>)> iterate_handles, function< bool(handle_t)> handle_in_range, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

void	vg::clip_stubs (MutablePathMutableHandleGraph *graph, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

void	vg::clip_contained_stubs (MutablePathMutableHandleGraph graph, PathPositionHandleGraph pp_graph, const vector< Region > &regions, SnarlManager &snarl_manager, bool include_endpoints, int64_t min_fragment_len, bool verbose)

void	vg::stubbify_ref_paths (MutablePathMutableHandleGraph *graph, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

Classes

Namespaces

Functions