hts_alignment_emitter.hpp File Reference

#include <mutex>
#include <thread>
#include <vector>
#include <deque>
#include <htslib/hfile.h>
#include <htslib/hts.h>
#include <htslib/sam.h>
#include <vg/vg.pb.h>
#include <vg/io/protobuf_emitter.hpp>
#include <vg/io/stream_multiplexer.hpp>
#include "handle.hpp"
#include "vg/io/alignment_emitter.hpp"

Classes
class	vg::HTSWriter
class	vg::HTSAlignmentEmitter
class	vg::SplicedHTSAlignmentEmitter

Namespaces
	vg

Functions
unique_ptr< AlignmentEmitter >	vg::get_alignment_emitter (const string &filename, const string &format, const vector< path_handle_t > &paths, size_t max_threads, const HandleGraph *graph, bool hts_raw, bool hts_spliced)
vector< path_handle_t >	vg::get_sequence_dictionary (const string &filename, const PathPositionHandleGraph &graph)
vector< pair< string, int64_t > >	vg::extract_path_metadata (const vector< path_handle_t > &paths, const PathPositionHandleGraph &graph)