chain_items.cpp File Reference

#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_graph_lookback_bases, size_t max_read_lookback_bases)
std::vector< std::tuple< size_t, size_t, size_t > >	vg::algorithms::generate_zip_tree_transitions (const std::vector< SnarlDistanceIndexClusterer::Seed > &seeds, const ZipCodeTree &zip_code_tree, size_t max_graph_lookback_bases, const std::unordered_map< size_t, size_t > &seed_to_starting, const std::unordered_map< size_t, size_t > &seed_to_ending)
std::vector< std::tuple< size_t, size_t, size_t, size_t > >	vg::algorithms::calculate_transition_read_distances (const std::vector< std::tuple< size_t, size_t, size_t >> &all_transitions, const VectorView< Anchor > &to_chain, size_t max_read_lookback_bases)
int	vg::algorithms::score_chain_gap (size_t distance_difference, size_t base_seed_length)
int	vg::algorithms::check_recombination (const TracedScore &from, const Anchor &to)
	If the current anchor shares paths with the chain, pay a penalty. More...
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, int recomb_penalty, 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, int recomb_penalty, 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, int recomb_penalty, 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...

Detailed Description

Non-template function implementations for chaining pieces of a read-to-graph alignment.