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"

Classes
class	vg::AlignmentEmitter
class	vg::NullAlignmentEmitter
class	vg::TSVAlignmentEmitter
class	vg::HTSAlignmentEmitter
class	vg::SplicedHTSAlignmentEmitter
class	vg::VGAlignmentEmitter

Namespaces
	vg

Functions
unique_ptr< AlignmentEmitter >	vg::get_alignment_emitter (const string &filename, const string &format, const map< string, int64_t > &path_length, size_t max_threads, const PathPositionHandleGraph *splicing_graph)

Detailed Description

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