vg
tools for working with variation graphs
Namespaces | Functions | Variables
alignment_io.hpp File Reference
#include <iostream>
#include <functional>
#include <zlib.h>
#include <vg/vg.pb.h>
#include "htslib/hfile.h"
#include "htslib/hts.h"
#include "htslib/sam.h"
#include "htslib/vcf.h"
#include "handlegraph/handle_graph.hpp"
#include "vg/io/gafkluge.hpp"

Namespaces

 vg
 
 vg::io
 

Functions

size_t vg::io::unpaired_for_each_parallel (function< bool(Alignment &)> get_read_if_available, function< void(Alignment &)> lambda, uint64_t batch_size)
 
size_t vg::io::paired_for_each_parallel_after_wait (function< bool(Alignment &, Alignment &)> get_pair_if_available, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)
 
bool vg::io::get_next_alignment_from_gaf (const HandleGraph &graph, htsFile *fp, kstring_t &s_buffer, gafkluge::GafRecord &g_buffer, Alignment &alignment)
 
bool vg::io::get_next_interleaved_alignment_pair_from_gaf (const HandleGraph &graph, htsFile *fp, kstring_t &s_buffer, gafkluge::GafRecord &g_buffer, Alignment &mate1, Alignment &mate2)
 
size_t vg::io::gaf_unpaired_for_each (const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda)
 
size_t vg::io::gaf_paired_interleaved_for_each (const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda)
 
size_t vg::io::gaf_unpaired_for_each_parallel (const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size)
 
size_t vg::io::gaf_paired_interleaved_for_each_parallel (const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size)
 
size_t vg::io::gaf_paired_interleaved_for_each_parallel_after_wait (const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)
 
gafkluge::GafRecord vg::io::alignment_to_gaf (const HandleGraph &graph, const Alignment &aln, bool cs_cigar, bool base_quals)
 
void vg::io::gaf_to_alignment (const HandleGraph &graph, const gafkluge::GafRecord &gaf, Alignment &aln)
 
short vg::io::quality_char_to_short (char c)
 
char vg::io::quality_short_to_char (short i)
 
string vg::io::string_quality_char_to_short (const string &quality)
 
string vg::io::string_quality_short_to_char (const string &quality)
 
void vg::io::alignment_quality_char_to_short (Alignment &alignment)
 
void vg::io::alignment_quality_short_to_char (Alignment &alignment)
 

Variables

const uint64_t vg::io::DEFAULT_PARALLEL_BATCHSIZE = 512