vg
tools for working with variation graphs
Classes | Namespaces | Functions
gapless_extender.cpp File Reference
#include "gapless_extender.hpp"
#include <algorithm>
#include <cstring>
#include <queue>
#include <set>
#include <stack>

Classes

struct  vg::state_hash
 

Namespaces

 vg
 

Functions

template<class Element >
void vg::in_place_subvector (std::vector< Element > &vec, size_t head, size_t tail)
 
void vg::set_score (GaplessExtension &extension, const Aligner *aligner)
 
void vg::match_initial (GaplessExtension &match, const std::string &seq, gbwtgraph::GBWTGraph::view_type target)
 
size_t vg::match_forward (GaplessExtension &match, const std::string &seq, gbwtgraph::GBWTGraph::view_type target, uint32_t mismatch_limit)
 
void vg::match_backward (GaplessExtension &match, const std::string &seq, gbwtgraph::GBWTGraph::view_type target, uint32_t mismatch_limit)
 
void vg::handle_full_length (const HandleGraph &graph, std::vector< GaplessExtension > &result, double overlap_threshold)
 
void vg::remove_duplicates (std::vector< GaplessExtension > &result)
 
void vg::find_mismatches (const std::string &seq, const gbwtgraph::CachedGBWTGraph &graph, std::vector< GaplessExtension > &result)
 
size_t vg::interval_length (std::pair< size_t, size_t > interval)
 
std::vector< handle_t > vg::get_path (const std::vector< handle_t > &first, handle_t second)
 
std::vector< handle_t > vg::get_path (handle_t first, const std::vector< handle_t > &second)
 
std::vector< handle_t > vg::get_path (const std::vector< handle_t > &first, gbwt::node_type second)
 
std::vector< handle_t > vg::get_path (gbwt::node_type reverse_first, const std::vector< handle_t > &second)
 
bool vg::trim_mismatches (GaplessExtension &extension, const gbwtgraph::CachedGBWTGraph &graph, const Aligner &aligner)