vg
tools for working with variation graphs
Classes | Namespaces | Functions
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.