utility.cpp File Reference

#include "utility.hpp"
#include "statistics.hpp"
#include <set>
#include <mutex>
#include <dirent.h>
#include <thread>
#include <cstdio>
#include <cmath>
#include <fstream>
#include <iostream>
#include <cctype>
#include <gcsa/utils.h>
#include <gbwt/utils.h>
#include <xg.hpp>

Classes
struct	vg::temp_file::Handler

Namespaces
	vg
	vg::temp_file

Functions
char	vg::reverse_complement (const char &c)
string	vg::reverse_complement (const string &seq)
void	vg::reverse_complement_in_place (string &seq)
bool	vg::is_all_n (const string &seq)
double	vg::get_fraction_of_ns (const string &seq)
int	vg::get_thread_count (void)
void	vg::choose_good_thread_count ()
std::vector< std::string > &	vg::split_delims (const std::string &s, const std::string &delims, std::vector< std::string > &elems, size_t max_cuts)
std::vector< std::string >	vg::split_delims (const std::string &s, const std::string &delims, size_t max_cuts)
bool	vg::starts_with (const std::string &value, const std::string &prefix)
	Check if a string starts with another string. More...
const std::string	vg::sha1sum (const std::string &data)
const std::string	vg::sha1head (const std::string &data, size_t head)
string	vg::wrap_text (const string &str, size_t width)
bool	vg::is_number (const std::string &s)
bool	vg::isATGC (const char &b)
	Return true if a character is an uppercase A, C, G, or T, and false otherwise. More...
bool	vg::allATGC (const string &s)
bool	vg::allATGCN (const string &s)
string	vg::nonATGCNtoN (const string &s)
string	vg::allAmbiguousToN (const string &s)
string	vg::toUppercase (const string &s)
void	vg::toUppercaseInPlace (string &s)
void	vg::write_fasta_sequence (const std::string &name, const std::string &sequence, ostream &os, size_t width)
string	vg::temp_file::create (const string &base)
	Create a temporary file starting with the given base name. More...
string	vg::temp_file::create ()
	Create a temporary file. More...
string	vg::temp_file::create_directory ()
	Create a temporary directory. More...
void	vg::temp_file::remove (const string &filename)
void	vg::temp_file::forget ()
	Forget about all current temporary files and directories without deleting them. More...
void	vg::temp_file::set_system_dir ()
void	vg::temp_file::set_dir (const string &new_temp_dir)
string	vg::temp_file::get_dir ()
	Get the current location for temporary files and directories. More...
string	vg::get_or_make_variant_id (const vcflib::Variant &variant)
string	vg::make_variant_id (const vcflib::Variant &variant)
vector< size_t >	vg::range_vector (size_t begin, size_t end)
	Vector containing positive integer values in [begin, end) More...
std::vector< size_t >	vg::stack_permutations (const std::vector< size_t > &bottom, const std::vector< size_t > &top)
	Apply one permutation on top of another. Retutn the combined permutation. More...
bool	vg::have_input_file (int &optind, int argc, char **argv)
	Return true if there's a command line argument (i.e. input file name) waiting to be processed. More...
void	vg::get_input_file (int &optind, int argc, char **argv, function< void(istream &)> callback)
string	vg::get_input_file_name (int &optind, int argc, char **argv, bool test_open)
string	vg::get_output_file_name (int &optind, int argc, char **argv)
void	vg::get_input_file (const string &file_name, function< void(istream &)> callback)
pair< string, string >	vg::split_ext (const string &filename)
	Split off the extension from a filename and return both parts. More...
string	vg::file_base_name (const string &filename)
	Get the base name of a filename (without the directory and the extension). More...
bool	vg::file_exists (const string &filename)
void	vg::create_ref_allele (vcflib::Variant &variant, const std::string &allele)
int	vg::add_alt_allele (vcflib::Variant &variant, const std::string &allele)
size_t	vg::integer_power (uint64_t base, uint64_t exponent)
	Computes base^exponent in log(exponent) time. More...
size_t	vg::modular_exponent (uint64_t base, uint64_t exponent, uint64_t modulus)
default_random_engine	vg::random_sequence_gen (102)
string	vg::random_sequence (size_t length)
	Returns a uniformly random DNA sequence of the given length. More...
string	vg::pseudo_random_sequence (size_t length, uint64_t seed)
	Returns a uniformly random DNA sequence sequence deterministically from a seed. More...
string	vg::replace_in_string (string subject, const string &search, const string &replace)
string	vg::percent_url_encode (const string &seq)
	Escape "%" to "%25". More...
bool	vg::deterministic_flip (LazyRNG &rng)
	Flip a coin with 50% probability against the given RNG. More...
unordered_map< id_t, pair< id_t, bool > >	vg::overlay_node_translations (const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, pair< id_t, bool >> &under)
	Compose the translations from two graph operations, both of which involved oriented transformations. More...
unordered_map< id_t, pair< id_t, bool > >	vg::overlay_node_translations (const unordered_map< id_t, id_t > &over, const unordered_map< id_t, pair< id_t, bool >> &under)
	Compose the translations from two graph operations, the first of which involved oriented transformations. More...
unordered_map< id_t, pair< id_t, bool > >	vg::overlay_node_translations (const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, id_t > &under)
	Compose the translations from two graph operations, the second of which involved oriented transformations. More...
unordered_map< id_t, id_t >	vg::overlay_node_translations (const unordered_map< id_t, id_t > &over, const unordered_map< id_t, id_t > &under)
	Compose the translations from two graph operations, neither of which involved oriented transformations. More...
template<>
bool	vg::parse (const string &arg, double &dest)
template<>
bool	vg::parse (const string &arg, std::regex &dest)
template<>
bool	vg::parse (const string &arg, pos_t &dest)