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| | CachedPackedTraversalSupportFinder (const Packer &packer, SnarlManager &snarl_manager, size_t cache_size=500000) |
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| virtual | ~CachedPackedTraversalSupportFinder () |
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| virtual Support | get_edge_support (id_t from, bool from_reverse, id_t to, bool to_reverse) const |
| | Support of an edge. More...
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| virtual Support | get_min_node_support (id_t node) const |
| | Minimum support of a node. More...
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| virtual Support | get_avg_node_support (id_t node) const |
| | Average support of a node. More...
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| virtual size_t | get_avg_node_mapq (id_t node) const |
| | Average MAPQ of reads that map to a node. More...
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| | PackedTraversalSupportFinder (const Packer &packer, SnarlManager &snarl_manager) |
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| virtual | ~PackedTraversalSupportFinder () |
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| virtual Support | get_edge_support (const edge_t &edge) const |
| | Support of an edge. More...
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| | TraversalSupportFinder (const HandleGraph &graph, SnarlManager &snarl_manager) |
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| virtual | ~TraversalSupportFinder () |
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| virtual int64_t | get_edge_length (const edge_t &edge, const unordered_map< id_t, size_t > &ref_offsets) const |
| | Effective length of an edge. More...
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| virtual tuple< Support, Support, int > | get_child_support (const Snarl &snarl) const |
| | Use node or edge support as proxy for child support (as was done in original calling code) More...
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| virtual Support | get_traversal_support (const SnarlTraversal &traversal) const |
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| virtual vector< Support > | get_traversal_genotype_support (const vector< SnarlTraversal > &traversals, const vector< int > &genotype, const set< int > &other_trav_subset, int ref_trav_idx=-1, int *max_trav_size=nullptr) |
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| virtual vector< Support > | get_traversal_set_support (const vector< SnarlTraversal > &traversals, const vector< int > &shared_travs, const vector< Support > &shared_support, const set< int > &tgt_travs, bool exclusive_only, const vector< int > &exclusive_count_travs, const vector< Support > &exclusive_count_support, int ref_trav_idx=-1, int *max_trav_size=nullptr) const |
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| virtual vector< int > | get_traversal_sizes (const vector< SnarlTraversal > &traversals) const |
| | Get the total length of all nodes in the traversal. More...
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| virtual vector< double > | get_traversal_mapqs (const vector< SnarlTraversal > &traversals) const |
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| virtual size_t | get_average_traversal_support_switch_threshold () const |
| | Get the average traversal support thresholdek. More...
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| unordered_map< id_t, size_t > | get_ref_offsets (const SnarlTraversal &ref_trav) const |
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| virtual void | set_support_switch_threshold (size_t trav_thresh, size_t node_thresh) |
| | set the threshold More...
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| virtual void | set_min_bp_edge_override (bool bp_override) |
| | set the breakpoint stricter upper override More...
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| virtual void | apply_min_bp_edge_override (const vector< SnarlTraversal > &traversals, const set< int > &tgt_travs, vector< Support > &supports, int ref_trav_idx) const |
| | apply the override to a set of traversals More...
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Add a caching overlay to the PackedTravesalSupportFinder to avoid frequent base queries which can become expensive. Even caching the edges seems to have an impact
Public Member Functions inherited from vg::PackedTraversalSupportFinder