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 "protobuf_emitter.hpp"
#include "stream_multiplexer.hpp"
#include <handlegraph/handle_graph.hpp>
#include <handlegraph/named_node_back_translation.hpp>

Classes
class	vg::io::AlignmentEmitter
class	vg::io::NullAlignmentEmitter
class	vg::io::TSVAlignmentEmitter
class	vg::io::VGAlignmentEmitter
class	vg::io::GafAlignmentEmitter

Namespaces
	vg
	vg::io

Typedefs
using	vg::io::handle_t = handlegraph::handle_t
using	vg::io::nid_t = handlegraph::nid_t
using	vg::io::path_handle_t = handlegraph::path_handle_t
using	vg::io::step_handle_t = handlegraph::step_handle_t
using	vg::io::edge_t = handlegraph::edge_t
using	vg::io::HandleGraph = handlegraph::HandleGraph

Functions
unique_ptr< AlignmentEmitter >	vg::io::get_non_hts_alignment_emitter (const string &filename, const string &format, const map< string, int64_t > &path_length, size_t max_threads, const HandleGraph *graph, const handlegraph::NamedNodeBackTranslation *translate_through)

Detailed Description

Defines a system for emitting alignments and groups of alignments in multiple formats.