vg
tools for working with variation graphs
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Classes | |
class | SubHandleGraph |
Functions | |
void | append_handle_graph (const HandleGraph *from, MutableHandleGraph *into) |
void | append_path_handle_graph (const PathHandleGraph *from, MutablePathMutableHandleGraph *into, bool only_connect_path_tips) |
unordered_set< nid_t > | apply_orientations (MutableHandleGraph *graph, const vector< handle_t > &orientations) |
bool | are_equivalent (const HandleGraph *graph_1, const HandleGraph *graph_2, bool verbose) |
bool | are_equivalent_with_paths (const PathHandleGraph *graph_1, const PathHandleGraph *graph_2, bool verbose) |
void | copy_handle_graph (const HandleGraph *from, MutableHandleGraph *into) |
void | copy_path_handle_graph (const PathHandleGraph *from, MutablePathMutableHandleGraph *into) |
void | copy_path (const PathHandleGraph *from, const path_handle_t &path, MutablePathHandleGraph *into) |
tuple< vector< handle_t >, unordered_map< handle_t, size_t >, bool > | count_walks_through_nodes (const HandleGraph *graph) |
size_t | count_walks (const HandleGraph *graph) |
unordered_map< nid_t, nid_t > | dagify (const HandleGraph *graph, MutableHandleGraph *into, size_t min_preserved_path_length) |
bool | dijkstra (const HandleGraph *g, handle_t start, function< bool(const handle_t &, size_t)> reached_callback, bool traverse_leftward) |
bool | dijkstra (const HandleGraph *g, const unordered_set< handle_t > &starts, function< bool(const handle_t &, size_t)> reached_callback, bool traverse_leftward) |
vector< handle_t > | eades_algorithm (const HandleGraph *graph) |
void | extend (const HandleGraph *source, MutableHandleGraph *into) |
unordered_map< handle_t, size_t > | find_shortest_paths (const HandleGraph *g, handle_t start, bool traverse_leftward) |
vector< handle_t > | head_nodes (const HandleGraph *g) |
vector< handle_t > | tail_nodes (const HandleGraph *g) |
vector< handle_t > | find_tips (const HandleGraph *g) |
bool | is_acyclic (const HandleGraph *graph) |
bool | is_directed_acyclic (const HandleGraph *graph) |
bool | is_single_stranded (const HandleGraph *graph) |
vector< handle_t > | single_stranded_orientation (const HandleGraph *graph) |
unordered_set< nid_t > | make_single_stranded (MutableHandleGraph *graph) |
void | reverse_complement_graph (const HandleGraph *source, MutableHandleGraph *into) |
unordered_map< handle_t, handle_t > | split_strands (const HandleGraph *source, MutableHandleGraph *into) |
void | dfs (const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const function< bool(void)> &break_fn, const function< void(const edge_t &)> &edge_fn, const function< void(const edge_t &)> &tree_fn, const function< void(const edge_t &)> &edge_curr_fn, const function< void(const edge_t &)> &edge_cross_fn, const vector< handle_t > &sources, const unordered_set< handle_t > &sinks) |
void | dfs (const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const vector< handle_t > &sources, const unordered_set< handle_t > &sinks) |
void | dfs (const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const function< bool(void)> &break_fn) |
vector< unordered_set< nid_t > > | strongly_connected_components (const HandleGraph *handle_graph) |
vector< handle_t > | topological_order (const HandleGraph *g) |
vector< handle_t > | lazy_topological_order_internal (const HandleGraph *g, bool lazier) |
vector< handle_t > | lazy_topological_order (const HandleGraph *g) |
vector< handle_t > | lazier_topological_order (const HandleGraph *g) |
void | unchop (handlegraph::MutablePathDeletableHandleGraph *graph) |
void | chop (handlegraph::MutableHandleGraph *graph, size_t max_node_length) |
vector< unordered_set< nid_t > > | weakly_connected_components (const HandleGraph *graph) |
vector< pair< unordered_set< nid_t >, vector< handle_t > > > | weakly_connected_components_with_tips (const HandleGraph *graph) |
bool | is_weakly_connected (const HandleGraph *graph) |
void handlegraph::algorithms::append_handle_graph | ( | const HandleGraph * | from, |
MutableHandleGraph * | into | ||
) |
void handlegraph::algorithms::append_path_handle_graph | ( | const PathHandleGraph * | from, |
MutablePathMutableHandleGraph * | into, | ||
bool | only_connect_path_tips | ||
) |
unordered_set<nid_t> handlegraph::algorithms::apply_orientations | ( | MutableHandleGraph * | graph, |
const vector< handle_t > & | orientations | ||
) |
bool handlegraph::algorithms::are_equivalent | ( | const HandleGraph * | graph_1, |
const HandleGraph * | graph_2, | ||
bool | verbose | ||
) |
bool handlegraph::algorithms::are_equivalent_with_paths | ( | const PathHandleGraph * | graph_1, |
const PathHandleGraph * | graph_2, | ||
bool | verbose | ||
) |
void handlegraph::algorithms::chop | ( | handlegraph::MutableHandleGraph * | graph, |
size_t | max_node_length | ||
) |
void handlegraph::algorithms::copy_handle_graph | ( | const HandleGraph * | from, |
MutableHandleGraph * | into | ||
) |
void handlegraph::algorithms::copy_path | ( | const PathHandleGraph * | from, |
const path_handle_t & | path, | ||
MutablePathHandleGraph * | into | ||
) |
void handlegraph::algorithms::copy_path_handle_graph | ( | const PathHandleGraph * | from, |
MutablePathMutableHandleGraph * | into | ||
) |
size_t handlegraph::algorithms::count_walks | ( | const HandleGraph * | graph | ) |
tuple<vector<handle_t>, unordered_map<handle_t, size_t>, bool> handlegraph::algorithms::count_walks_through_nodes | ( | const HandleGraph * | graph | ) |
unordered_map<nid_t, nid_t> handlegraph::algorithms::dagify | ( | const HandleGraph * | graph, |
MutableHandleGraph * | into, | ||
size_t | min_preserved_path_length | ||
) |
void handlegraph::algorithms::dfs | ( | const HandleGraph & | graph, |
const function< void(const handle_t &)> & | handle_begin_fn, | ||
const function< void(const handle_t &)> & | handle_end_fn, | ||
const function< bool(void)> & | break_fn | ||
) |
void handlegraph::algorithms::dfs | ( | const HandleGraph & | graph, |
const function< void(const handle_t &)> & | handle_begin_fn, | ||
const function< void(const handle_t &)> & | handle_end_fn, | ||
const function< bool(void)> & | break_fn, | ||
const function< void(const edge_t &)> & | edge_fn, | ||
const function< void(const edge_t &)> & | tree_fn, | ||
const function< void(const edge_t &)> & | edge_curr_fn, | ||
const function< void(const edge_t &)> & | edge_cross_fn, | ||
const vector< handle_t > & | sources, | ||
const unordered_set< handle_t > & | sinks | ||
) |
void handlegraph::algorithms::dfs | ( | const HandleGraph & | graph, |
const function< void(const handle_t &)> & | handle_begin_fn, | ||
const function< void(const handle_t &)> & | handle_end_fn, | ||
const vector< handle_t > & | sources, | ||
const unordered_set< handle_t > & | sinks | ||
) |
bool handlegraph::algorithms::dijkstra | ( | const HandleGraph * | g, |
const unordered_set< handle_t > & | starts, | ||
function< bool(const handle_t &, size_t)> | reached_callback, | ||
bool | traverse_leftward | ||
) |
bool handlegraph::algorithms::dijkstra | ( | const HandleGraph * | g, |
handle_t | start, | ||
function< bool(const handle_t &, size_t)> | reached_callback, | ||
bool | traverse_leftward | ||
) |
vector<handle_t> handlegraph::algorithms::eades_algorithm | ( | const HandleGraph * | graph | ) |
void handlegraph::algorithms::extend | ( | const HandleGraph * | source, |
MutableHandleGraph * | into | ||
) |
unordered_map<handle_t, size_t> handlegraph::algorithms::find_shortest_paths | ( | const HandleGraph * | g, |
handle_t | start, | ||
bool | traverse_leftward | ||
) |
vector<handle_t> handlegraph::algorithms::find_tips | ( | const HandleGraph * | g | ) |
vector<handle_t> handlegraph::algorithms::head_nodes | ( | const HandleGraph * | g | ) |
bool handlegraph::algorithms::is_acyclic | ( | const HandleGraph * | graph | ) |
bool handlegraph::algorithms::is_directed_acyclic | ( | const HandleGraph * | graph | ) |
bool handlegraph::algorithms::is_single_stranded | ( | const HandleGraph * | graph | ) |
bool handlegraph::algorithms::is_weakly_connected | ( | const HandleGraph * | graph | ) |
vector<handle_t> handlegraph::algorithms::lazier_topological_order | ( | const HandleGraph * | g | ) |
vector<handle_t> handlegraph::algorithms::lazy_topological_order | ( | const HandleGraph * | g | ) |
vector<handle_t> handlegraph::algorithms::lazy_topological_order_internal | ( | const HandleGraph * | g, |
bool | lazier | ||
) |
unordered_set<nid_t> handlegraph::algorithms::make_single_stranded | ( | MutableHandleGraph * | graph | ) |
void handlegraph::algorithms::reverse_complement_graph | ( | const HandleGraph * | source, |
MutableHandleGraph * | into | ||
) |
vector<handle_t> handlegraph::algorithms::single_stranded_orientation | ( | const HandleGraph * | graph | ) |
unordered_map<handle_t, handle_t> handlegraph::algorithms::split_strands | ( | const HandleGraph * | source, |
MutableHandleGraph * | into | ||
) |
vector<unordered_set<nid_t> > handlegraph::algorithms::strongly_connected_components | ( | const HandleGraph * | handle_graph | ) |
vector<handle_t> handlegraph::algorithms::tail_nodes | ( | const HandleGraph * | g | ) |
vector<handle_t> handlegraph::algorithms::topological_order | ( | const HandleGraph * | g | ) |
void handlegraph::algorithms::unchop | ( | handlegraph::MutablePathDeletableHandleGraph * | graph | ) |
vector<unordered_set<nid_t> > handlegraph::algorithms::weakly_connected_components | ( | const HandleGraph * | graph | ) |
vector<pair<unordered_set<nid_t>, vector<handle_t> > > handlegraph::algorithms::weakly_connected_components_with_tips | ( | const HandleGraph * | graph | ) |