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vg
tools for working with variation graphs
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#include "chain_items.hpp"#include "crash.hpp"#include <handlegraph/algorithms/dijkstra.hpp>#include <structures/immutable_list.hpp>#include <structures/min_max_heap.hpp>Namespaces | |
| vg | |
| vg::algorithms | |
Functions | |
| ostream & | vg::algorithms::operator<< (ostream &out, const Anchor &anchor) |
| Explain an Anchor to the given stream. More... | |
| ostream & | vg::algorithms::operator<< (ostream &out, const TracedScore &value) |
| Print operator. More... | |
| void | vg::algorithms::sort_anchor_indexes (const std::vector< Anchor > &items, std::vector< size_t > &indexes) |
| transition_iterator | vg::algorithms::lookback_transition_iterator (size_t max_lookback_bases, size_t min_lookback_items, size_t lookback_item_hard_cap) |
| transition_iterator | vg::algorithms::zip_tree_transition_iterator (const std::vector< SnarlDistanceIndexClusterer::Seed > &seeds, const ZipCodeTree &zip_code_tree, size_t max_lookback_bases) |
| int | vg::algorithms::score_chain_gap (size_t distance_difference, size_t base_seed_length) |
| TracedScore | vg::algorithms::chain_items_dp (vector< TracedScore > &chain_scores, const VectorView< Anchor > &to_chain, const SnarlDistanceIndex &distance_index, const HandleGraph &graph, int gap_open, int gap_extension, const transition_iterator &for_each_transition, int item_bonus, double item_scale, double gap_scale, double points_per_possible_match, size_t max_indel_bases, bool show_work) |
| vector< pair< vector< size_t >, int > > | vg::algorithms::chain_items_traceback (const vector< TracedScore > &chain_scores, const VectorView< Anchor > &to_chain, const TracedScore &best_past_ending_score_ever, int item_bonus, double item_scale, size_t max_tracebacks) |
| vector< pair< int, vector< size_t > > > | vg::algorithms::find_best_chains (const VectorView< Anchor > &to_chain, const SnarlDistanceIndex &distance_index, const HandleGraph &graph, int gap_open, int gap_extension, size_t max_chains, const transition_iterator &for_each_transition, int item_bonus, double item_scale, double gap_scale, double points_per_possible_match, size_t max_indel_bases, bool show_work) |
| pair< int, vector< size_t > > | vg::algorithms::find_best_chain (const VectorView< Anchor > &to_chain, const SnarlDistanceIndex &distance_index, const HandleGraph &graph, int gap_open, int gap_extension, const transition_iterator &for_each_transition, int item_bonus, double item_scale, double gap_scale, double points_per_possible_match, size_t max_indel_bases) |
| int | vg::algorithms::score_best_chain (const VectorView< Anchor > &to_chain, const SnarlDistanceIndex &distance_index, const HandleGraph &graph, int gap_open, int gap_extension) |
| size_t | vg::algorithms::get_graph_distance (const Anchor &from, const Anchor &to, const SnarlDistanceIndex &distance_index, const HandleGraph &graph, size_t distance_limit=std::numeric_limits< size_t >::max()) |
| Get distance in the graph, or std::numeric_limits<size_t>::max() if unreachable or beyond the limit. More... | |
| size_t | vg::algorithms::get_read_distance (const Anchor &from, const Anchor &to) |
| Get distance in the read, or std::numeric_limits<size_t>::max() if unreachable. More... | |
Non-template function implementations for chaining pieces of a read-to-graph alignment.
1.8.17