Augmented Graph that holds some Support annotation data specific to vg call. More...
#include <genotypekit.hpp>
Inheritance diagram for vg::SupportAugmentedGraph:
Public Member Functions | |
| virtual bool | has_supports () const |
| virtual Support | get_support (id_t node) |
| virtual Support | get_support (edge_t edge) |
| virtual void | clear () |
| void | load_supports (istream &in_file) |
| void | load_pack_as_supports (const string &pack_file_name, const HandleGraph *vectorizable_graph) |
| void | write_supports (ostream &out_file) |
 Public Member Functions inherited from vg::AugmentedGraph | |
| pair< const Edge *, bool > | base_edge (const Edge *augmented_edge) |
| bool | is_novel_node (const Node *augmented_node) |
| bool | is_novel_edge (const Edge *augmented_edge) |
| bool | has_base_graph () const |
| vector< const Alignment * > | get_alignments (id_t node_id) const |
| vector< const Alignment * > | get_alignments (pair< NodeSide, NodeSide >) const |
| vector< const Alignment * > | get_alignments () const |
| Get all the embedded alignments. More... | |
| void | augment_from_alignment_edits (vector< Alignment > &alignments, bool unique_names=true, bool leave_edits=false) |
| void | load_translations (istream &in_file) |
| void | write_translations (ostream &out_file) |
Public Attributes | |
| map< id_t, Support > | node_supports |
| unordered_map< edge_t, Support > | edge_supports |
| Public Attributes inherited from vg::AugmentedGraph | |
| VG | graph |
| This holds all the new nodes and edges. More... | |
| VG * | base_graph = nullptr |
| This holds the base graph (only required for mapping edges) More... | |
| Translator | translator |
| Translations back to the base graph. More... | |
Additional Inherited Members | |
| Protected Attributes inherited from vg::AugmentedGraph | |
| vector< Alignment > | embedded_alignments |
| unordered_map< id_t, vector< Alignment * > > | alignments_by_node |
| pair_hash_map< pair< NodeSide, NodeSide >, vector< Alignment * > > | alignments_by_edge |
Detailed Description
Member Function Documentation
◆ clear()
|
virtual |
Clear the contents.
Reimplemented from vg::AugmentedGraph.
◆ get_support() [1/2]
Get the Support for a given Edge, or 0 if it has no recorded support.
Reimplemented from vg::AugmentedGraph.
◆ get_support() [2/2]
Get the Support for a given Node, or 0 if it has no recorded support.
Reimplemented from vg::AugmentedGraph.
◆ has_supports()
|
virtual |
Return true if we have support information, and false otherwise.
Reimplemented from vg::AugmentedGraph.
◆ load_pack_as_supports()
| void vg::SupportAugmentedGraph::load_pack_as_supports | ( | const string & | pack_file_name, |
| const HandleGraph * | vectorizable_graph | ||
| ) |
Read the suppors from output of vg pack Everything put in forward support, average used for nodes Graph must implement VectorizableHandleGraph
◆ load_supports()
| void vg::SupportAugmentedGraph::load_supports | ( | istream & | in_file | ) |
Read the supports from protobuf.
◆ write_supports()
| void vg::SupportAugmentedGraph::write_supports | ( | ostream & | out_file | ) |
Write the supports to protobuf
Member Data Documentation
◆ edge_supports
◆ node_supports
The documentation for this struct was generated from the following files:
- src/genotypekit.hpp
- src/genotypekit.cpp
