vg
tools for working with variation graphs
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#include <subgraph_overlay.hpp>
Public Member Functions | |
PathSubgraphOverlay (const PathHandleGraph *backing, const unordered_set< nid_t > *node_subset) | |
virtual | ~PathSubgraphOverlay () |
virtual size_t | get_path_count () const |
Returns the number of paths stored in the graph. | |
virtual bool | has_path (const std::string &path_name) const |
Determine if a path name exists and is legal to get a path handle for. | |
virtual path_handle_t | get_path_handle (const std::string &path_name) const |
virtual std::string | get_path_name (const path_handle_t &path_handle) const |
Look up the name of a path from a handle to it. | |
virtual bool | get_is_circular (const path_handle_t &path_handle) const |
Look up whether a path is circular. | |
virtual size_t | get_step_count (const path_handle_t &path_handle) const |
Returns the number of node steps in the path. | |
virtual handle_t | get_handle_of_step (const step_handle_t &step_handle) const |
Get a node handle (node ID and orientation) from a handle to an step on a path. | |
virtual path_handle_t | get_path_handle_of_step (const step_handle_t &step_handle) const |
Returns a handle to the path that an step is on. | |
virtual step_handle_t | path_begin (const path_handle_t &path_handle) const |
virtual step_handle_t | path_end (const path_handle_t &path_handle) const |
virtual step_handle_t | path_back (const path_handle_t &path_handle) const |
virtual step_handle_t | path_front_end (const path_handle_t &path_handle) const |
virtual bool | has_next_step (const step_handle_t &step_handle) const |
Returns true if the step is not the last step in a non-circular path. | |
virtual bool | has_previous_step (const step_handle_t &step_handle) const |
Returns true if the step is not the first step in a non-circular path. | |
virtual step_handle_t | get_next_step (const step_handle_t &step_handle) const |
virtual step_handle_t | get_previous_step (const step_handle_t &step_handle) const |
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SubgraphOverlay (const HandleGraph *backing, const unordered_set< nid_t > *node_subset) | |
virtual | ~SubgraphOverlay () |
virtual bool | has_node (nid_t node_id) const |
Method to check if a node exists by ID. | |
virtual handle_t | get_handle (const nid_t &node_id, bool is_reverse=false) const |
Look up the handle for the node with the given ID in the given orientation. | |
virtual nid_t | get_id (const handle_t &handle) const |
Get the ID from a handle. | |
virtual bool | get_is_reverse (const handle_t &handle) const |
Get the orientation of a handle. | |
virtual handle_t | flip (const handle_t &handle) const |
Invert the orientation of a handle (potentially without getting its ID) | |
virtual size_t | get_length (const handle_t &handle) const |
Get the length of a node. | |
virtual std::string | get_sequence (const handle_t &handle) const |
virtual size_t | get_node_count () const |
Return the number of nodes in the graph. | |
virtual nid_t | min_node_id () const |
virtual nid_t | max_node_id () const |
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virtual | ~HandleGraph ()=default |
template<typename Iteratee > | |
bool | follow_edges (const handle_t &handle, bool go_left, const Iteratee &iteratee) const |
template<typename Iteratee > | |
bool | for_each_handle (const Iteratee &iteratee, bool parallel=false) const |
virtual size_t | get_degree (const handle_t &handle, bool go_left) const |
virtual bool | has_edge (const handle_t &left, const handle_t &right) const |
bool | has_edge (const edge_t &edge) const |
Convenient wrapper of has_edge for edge_t argument. | |
virtual size_t | get_edge_count () const |
virtual size_t | get_total_length () const |
virtual char | get_base (const handle_t &handle, size_t index) const |
virtual std::string | get_subsequence (const handle_t &handle, size_t index, size_t size) const |
handle_t | forward (const handle_t &handle) const |
Get the locally forward version of a handle. | |
edge_t | edge_handle (const handle_t &left, const handle_t &right) const |
handle_t | traverse_edge_handle (const edge_t &edge, const handle_t &left) const |
template<typename Iteratee > | |
bool | for_each_edge (const Iteratee &iteratee, bool parallel=false) const |
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virtual | ~PathHandleGraph ()=default |
virtual size_t | get_step_count (const handle_t &handle) const |
Returns the number of node steps on a handle. | |
template<typename Iteratee > | |
bool | for_each_path_handle (const Iteratee &iteratee) const |
template<typename Iteratee > | |
bool | for_each_step_on_handle (const handle_t &handle, const Iteratee &iteratee) const |
virtual std::vector< step_handle_t > | steps_of_handle (const handle_t &handle, bool match_orientation=false) const |
virtual bool | is_empty (const path_handle_t &path_handle) const |
Returns true if the given path is empty, and false otherwise. | |
PathForEachSocket | scan_path (const path_handle_t &path) const |
template<typename Iteratee > | |
bool | for_each_step_in_path (const path_handle_t &path, const Iteratee &iteratee) const |
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virtual | ~PathMetadata ()=default |
virtual PathSense | get_sense (const path_handle_t &handle) const |
What is the given path meant to be representing? | |
virtual std::string | get_sample_name (const path_handle_t &handle) const |
virtual std::string | get_locus_name (const path_handle_t &handle) const |
virtual size_t | get_haplotype (const path_handle_t &handle) const |
virtual size_t | get_phase_block (const path_handle_t &handle) const |
virtual subrange_t | get_subrange (const path_handle_t &handle) const |
template<typename Iteratee > | |
bool | for_each_path_of_sense (const PathSense &sense, const Iteratee &iteratee) const |
template<typename Iteratee > | |
bool | for_each_path_of_sample (const std::string &sample, const Iteratee &iteratee) const |
template<typename Iteratee > | |
bool | for_each_path_matching (const std::unordered_set< PathSense > *senses, const std::unordered_set< std::string > *samples, const std::unordered_set< std::string > *loci, const Iteratee &iteratee) const |
template<typename Iteratee > | |
bool | for_each_path_matching (const std::unordered_set< PathSense > &senses, const std::unordered_set< std::string > &samples, const std::unordered_set< std::string > &loci, const Iteratee &iteratee) const |
template<typename Iteratee > | |
bool | for_each_step_of_sense (const handle_t &visited, const PathSense &sense, const Iteratee &iteratee) const |
Protected Member Functions | |
virtual bool | for_each_path_handle_impl (const std::function< bool(const path_handle_t &)> &iteratee) const |
virtual bool | for_each_step_on_handle_impl (const handle_t &handle, const std::function< bool(const step_handle_t &)> &iteratee) const |
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virtual bool | follow_edges_impl (const handle_t &handle, bool go_left, const std::function< bool(const handle_t &)> &iteratee) const |
virtual bool | for_each_handle_impl (const std::function< bool(const handle_t &)> &iteratee, bool parallel=false) const |
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virtual bool | for_each_path_matching_impl (const std::unordered_set< PathSense > *senses, const std::unordered_set< std::string > *samples, const std::unordered_set< std::string > *loci, const std::function< bool(const path_handle_t &)> &iteratee) const |
virtual bool | for_each_step_of_sense_impl (const handle_t &visited, const PathSense &sense, const std::function< bool(const step_handle_t &)> &iteratee) const |
Protected Attributes | |
const PathHandleGraph * | backing_path_graph |
the backing path graph, just to not have to bother with dynamic cast | |
unordered_set< path_handle_t > | path_subset |
the subset of paths from the backing graph that are entirely contained within our subgraph | |
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const HandleGraph * | backing_graph |
the backing graph | |
const unordered_set< nid_t > * | node_subset |
nid_t | min_node = 0 |
keep min_node_id() and max_node_id() constant | |
nid_t | max_node = 0 |
Additional Inherited Members | |
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static PathSense | parse_sense (const std::string &path_name) |
static std::string | parse_sample_name (const std::string &path_name) |
static std::string | parse_locus_name (const std::string &path_name) |
static size_t | parse_haplotype (const std::string &path_name) |
static size_t | parse_phase_block (const std::string &path_name) |
static subrange_t | parse_subrange (const std::string &path_name) |
static void | parse_path_name (const std::string &path_name, PathSense &sense, std::string &sample, std::string &locus, size_t &haplotype, size_t &phase_block, subrange_t &subrange) |
Decompose a formatted path name into metadata. | |
static std::string | create_path_name (const PathSense &sense, const std::string &sample, const std::string &locus, const size_t &haplotype, const size_t &phase_block, const subrange_t &subrange) |
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static const std::string | NO_SAMPLE_NAME = "" |
static const std::string | NO_LOCUS_NAME = "" |
static const size_t | NO_HAPLOTYPE = std::numeric_limits<size_t>::max() |
static const size_t | NO_PHASE_BLOCK = std::numeric_limits<size_t>::max() |
static const subrange_t | NO_SUBRANGE {PathMetadata::NO_END_POSITION, PathMetadata::NO_END_POSITION} |
static const offset_t | NO_END_POSITION = std::numeric_limits<offset_t>::max() |
Present a PathHandleGraph that is a backing HandleGraph but restricted to a subset of nodes.
Warning: we don't yet have a subgraph interface. So we only consider paths from the backing graph that are fully contained in the subgraph.
vg::PathSubgraphOverlay::PathSubgraphOverlay | ( | const PathHandleGraph * | backing, |
const unordered_set< nid_t > * | node_subset | ||
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Make a new PathSubgraphOverlay. The backing graph must not be modified while the overlay exists.
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Execute a function on each path in the graph. If it returns false, stop iteration. Returns true if we finished and false if we stopped early.
Implements handlegraph::PathHandleGraph.
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Execute a function on each step of a handle in any path. If it returns false, stop iteration. Returns true if we finished and false if we stopped early.
Implements handlegraph::PathHandleGraph.
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Get a node handle (node ID and orientation) from a handle to an step on a path.
Implements handlegraph::PathHandleGraph.
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Look up whether a path is circular.
Implements handlegraph::PathHandleGraph.
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Returns a handle to the next step on the path. If the given step is the final step of a non-circular path, this method has undefined behavior. In a circular path, the "last" step will loop around to the "first" step.
Implements handlegraph::PathHandleGraph.
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Returns the number of paths stored in the graph.
Implements handlegraph::PathHandleGraph.
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Look up the path handle for the given path name. The path with that name must exist.
Implements handlegraph::PathHandleGraph.
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Returns a handle to the path that an step is on.
Implements handlegraph::PathHandleGraph.
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Look up the name of a path from a handle to it.
Implements handlegraph::PathHandleGraph.
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Returns a handle to the previous step on the path. If the given step is the first step of a non-circular path, this method has undefined behavior. In a circular path, it will loop around from the "first" step (i.e. the one returned by path_begin) to the "last" step.
Implements handlegraph::PathHandleGraph.
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Returns the number of node steps in the path.
Implements handlegraph::PathHandleGraph.
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Returns true if the step is not the last step in a non-circular path.
Implements handlegraph::PathHandleGraph.
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Determine if a path name exists and is legal to get a path handle for.
Implements handlegraph::PathHandleGraph.
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Returns true if the step is not the first step in a non-circular path.
Implements handlegraph::PathHandleGraph.
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Get a handle to the last step, which will be an arbitrary step in a circular path that we consider "last" based on our construction of the path. If the path is empty then the implementation must return the same value as path_front_end().
Implements handlegraph::PathHandleGraph.
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Get a handle to the first step, which will be an arbitrary step in a circular path that we consider "first" based on our construction of the path. If the path is empty, then the implementation must return the same value as path_end().
Implements handlegraph::PathHandleGraph.
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Get a handle to a fictitious position past the end of a path. This position is returned by get_next_step for the final step in a path in a non-circular path. Note: get_next_step will NEVER return this value for a circular path.
Implements handlegraph::PathHandleGraph.
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Get a handle to a fictitious position before the beginning of a path. This position is return by get_previous_step for the first step in a path in a non-circular path. Note: get_previous_step will NEVER return this value for a circular path.
Implements handlegraph::PathHandleGraph.
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the backing path graph, just to not have to bother with dynamic cast
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the subset of paths from the backing graph that are entirely contained within our subgraph