index_registry.cpp File Reference

#include "index_registry.hpp"
#include <algorithm>
#include <iostream>
#include <sstream>
#include <vector>
#include <map>
#include <random>
#include <thread>
#include <mutex>
#include <chrono>
#include <cctype>
#include <cstdio>
#include <cerrno>
#include <cstdlib>
#include <regex>
#include <omp.h>
#include <sys/stat.h>
#include <sys/wait.h>
#include <bdsg/hash_graph.hpp>
#include <bdsg/packed_graph.hpp>
#include <xg.hpp>
#include <gbwt/variants.h>
#include <gbwtgraph/index.h>
#include <gbwtgraph/gbwtgraph.h>
#include <gbwtgraph/gbz.h>
#include <gbwtgraph/path_cover.h>
#include <gbwtgraph/gfa.h>
#include <vg/io/vpkg.hpp>
#include <gcsa/gcsa.h>
#include <gcsa/algorithms.h>
#include <Fasta.h>
#include <htslib/tbx.h>
#include "vg.hpp"
#include "vg_set.hpp"
#include "handle.hpp"
#include "utility.hpp"
#include "constructor.hpp"
#include "hash_map.hpp"
#include "haplotype_indexer.hpp"
#include "phase_unfolder.hpp"
#include "gbwt_helper.hpp"
#include "gbwtgraph_helper.hpp"
#include "gcsa_helper.hpp"
#include "flat_file_back_translation.hpp"
#include "kmer.hpp"
#include "transcriptome.hpp"
#include "integrated_snarl_finder.hpp"
#include "snarl_distance_index.hpp"
#include "gfa.hpp"
#include "job_schedule.hpp"
#include "path.hpp"
#include "io/save_handle_graph.hpp"
#include "algorithms/gfa_to_handle.hpp"
#include "algorithms/prune.hpp"
#include "algorithms/component.hpp"
#include "algorithms/find_translation.hpp"

Namespaces
	std
	Hash functor to hash NodeSides using std::hash.
	vg

Functions
void	vg::copy_file (const string &from_fp, const string &to_fp)
int64_t	vg::get_file_size (const string &filename)
bool	vg::is_gzipped (const string &filename)
int64_t	vg::get_num_samples (const string &vcf_filename)
double	vg::approx_num_vars (const string &vcf_filename)
double	vg::format_multiplier ()
int64_t	vg::approx_graph_memory (const vector< string > &fasta_filenames, const vector< string > &vcf_filenames)
vector< int64_t >	vg::each_approx_graph_memory (const vector< string > &fasta_filenames, const vector< string > &vcf_filenames)
int64_t	vg::approx_graph_memory (const string &fasta_filename, const string &vcf_filename)
int64_t	vg::approx_graph_memory (const string &gfa_filename)
int64_t	vg::approx_gbwt_memory (const string &vcf_filename)
int64_t	vg::approx_graph_load_memory (const string &graph_filename)
bool	vg::transcript_file_nonempty (const string &transcripts)
vector< string >	vg::vcf_contigs (const string &filename)
size_t	vg::guess_parallel_gbwt_jobs (size_t node_count, size_t haplotype_count, size_t available_memory, size_t batch_size)
size_t	vg::xg_index_size (const xg::XG &index)
int	vg::execute_in_fork (const function< void(void)> &exec)