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

Namespaces

 vg
 

Functions

template<class Element >
void vg::in_place_subvector (std::vector< Element > &vec, size_t head, size_t tail)
 
void vg::match_initial (GaplessExtension &match, const std::string &seq, gbwtgraph::GBWTGraph::view_type target, const Aligner *aligner)
 
size_t vg::match_forward (GaplessExtension &match, const std::string &seq, gbwtgraph::GBWTGraph::view_type target, uint32_t mismatch_limit, const Aligner *aligner)
 
void vg::match_backward (GaplessExtension &match, const std::string &seq, gbwtgraph::GBWTGraph::view_type target, uint32_t mismatch_limit, const Aligner *aligner)
 
void vg::remove_duplicates (std::vector< GaplessExtension > &result)
 
void vg::find_mismatches (const std::string &seq, const gbwtgraph::GBWTGraph &graph, std::vector< GaplessExtension > &result)
 
size_t vg::interval_length (std::pair< size_t, size_t > interval)
 
bool vg::trim_mismatches (GaplessExtension &extension, const gbwtgraph::GBWTGraph &graph, const gbwt::CachedGBWT &cache, const Aligner &aligner)