hts_alignment_emitter.cpp File Reference

#include "hts_alignment_emitter.hpp"
#include "surjecting_alignment_emitter.hpp"
#include "back_translating_alignment_emitter.hpp"
#include "alignment.hpp"
#include "vg/io/json2pb.h"
#include "algorithms/find_translation.hpp"
#include "algorithms/md5_sum_path.hpp"
#include <vg/io/hfile_cppstream.hpp>
#include <vg/io/stream.hpp>
#include "crash.hpp"
#include <sstream>

Namespaces
	vg

Functions
unique_ptr< AlignmentEmitter >	vg::get_alignment_emitter (const string &filename, const string &format, const SequenceDictionary &paths, size_t max_threads, const HandleGraph *graph, int flags)
std::unordered_map< string, size_t >	vg::index_sequence_dictionary (const SequenceDictionary &paths)
SequenceDictionary	vg::get_sequence_dictionary (const string &filename, const vector< string > &path_names, const std::unordered_set< std::string > &reference_samples, const PathPositionHandleGraph &graph)