vg
tools for working with variation graphs
Classes | Namespaces | Functions
gfa_to_handle.hpp File Reference
#include <iostream>
#include <cctype>
#include <vector>
#include "../handle.hpp"

Classes

struct  vg::algorithms::GFAIDMapInfo
 
class  vg::algorithms::GFAParser
 
struct  vg::algorithms::GFAFormatError
 This exception will be thrown if the GFA data is not acceptable. More...
 
struct  vg::algorithms::GFADuplicatePathError
 

Namespaces

 vg
 
 vg::algorithms
 

Functions

void vg::algorithms::gfa_to_handle_graph (const string &filename, MutableHandleGraph *graph, GFAIDMapInfo *translation)
 
void vg::algorithms::gfa_to_handle_graph (const string &filename, MutableHandleGraph *graph, const string &translation_filename)
 Overload which serializes its translation to a file internally. More...
 
void vg::algorithms::gfa_to_handle_graph (istream &in, MutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr)
 Load a GFA from a stream (assumed not to be seekable or reopenable) into a HandleGraph. More...
 
void vg::algorithms::gfa_to_path_handle_graph (const string &filename, MutablePathMutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr, int64_t max_rgfa_rank=numeric_limits< int64_t >::max(), unordered_set< PathSense > *ignore_sense=nullptr)
 Same as gfa_to_handle_graph but also adds path elements from the GFA to the graph. More...
 
void vg::algorithms::gfa_to_path_handle_graph (const string &filename, MutablePathMutableHandleGraph *graph, int64_t max_rgfa_rank, const string &translation_filename, unordered_set< PathSense > *ignore_sense=nullptr)
 Overload which serializes its translation to a file internally. More...
 
void vg::algorithms::gfa_to_path_handle_graph (istream &in, MutablePathMutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr, int64_t max_rgfa_rank=numeric_limits< int64_t >::max(), unordered_set< PathSense > *ignore_sense=nullptr)
 Load a GFA from a stream (assumed not to be seekable or reopenable) into a PathHandleGraph. More...
 

Detailed Description

Defines algorithms for copying data from GFA files into handle graphs