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char | vg::reverse_complement (const char &c) |
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string | vg::reverse_complement (const string &seq) |
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void | vg::reverse_complement_in_place (string &seq) |
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bool | vg::is_all_n (const string &seq) |
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int | vg::get_thread_count (void) |
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string | vg::wrap_text (const string &str, size_t width) |
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bool | vg::is_number (const string &s) |
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std::vector< std::string > & | vg::split_delims (const std::string &s, const std::string &delims, std::vector< std::string > &elems) |
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std::vector< std::string > | vg::split_delims (const std::string &s, const std::string &delims) |
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const std::string | vg::sha1sum (const std::string &data) |
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const std::string | vg::sha1head (const std::string &data, size_t head) |
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bool | vg::allATGC (const string &s) |
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bool | vg::allATGCN (const string &s) |
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string | vg::nonATGCNtoN (const string &s) |
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string | vg::toUppercase (const string &s) |
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double | vg::median (std::vector< int > &v) |
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double | vg::stdev (const std::vector< double > &v) |
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void | vg::wellford_update (size_t &count, double &mean, double &M2, double new_val) |
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pair< double, double > | vg::wellford_mean_var (size_t count, double mean, double M2, bool sample_variance) |
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void | vg::write_fasta_sequence (const std::string &name, const std::string &sequence, ostream &os, size_t width) |
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template<typename T > |
double | vg::stdev (const T &v) |
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double | vg::phi (double x1, double x2) |
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double | vg::normal_inverse_cdf (double quantile) |
| Inverse CDF of a standard normal distribution. Must have 0 < quantile < 1. More...
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double | vg::add_log (double log_x, double log_y) |
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double | vg::subtract_log (double log_x, double log_y) |
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double | vg::ln_to_log10 (double ln) |
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double | vg::log10_to_ln (double l10) |
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double | vg::prob_to_logprob (double prob) |
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double | vg::logprob_to_prob (double logprob) |
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double | vg::logprob_add (double logprob1, double logprob2) |
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double | vg::logprob_invert (double logprob) |
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double | vg::phred_to_prob (int phred) |
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double | vg::prob_to_phred (double prob) |
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double | vg::phred_to_logprob (int phred) |
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double | vg::logprob_to_phred (double logprob) |
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double | vg::logprob_geometric_mean (double lnprob1, double lnprob2) |
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double | vg::phred_geometric_mean (double phred1, double phred2) |
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template<typename T > |
T | vg::normal_pdf (T x, T m, T s) |
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template<typename T , typename V > |
set< T > | vg::map_keys_to_set (const map< T, V > &m) |
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template<typename T > |
vector< T > | vg::pmax (const std::vector< T > &a, const std::vector< T > &b) |
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template<typename T > |
vector< T > | vg::vpmax (const std::vector< std::vector< T >> &vv) |
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template<typename Collection > |
Collection::value_type | vg::sum (const Collection &collection) |
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template<typename Collection > |
Collection::value_type | vg::logprob_sum (const Collection &collection) |
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string | vg::temp_file::create (const string &base) |
| Create a temporary file starting with the given base name. More...
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string | vg::temp_file::create () |
| Create a temporary file. More...
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void | vg::temp_file::remove (const string &filename) |
| Remove a temporary file. More...
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void | vg::temp_file::set_dir (const string &new_temp_dir) |
| Set a temp dir, overriding system defaults and environment variables. More...
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string | vg::temp_file::get_dir () |
| Get the current temp dir. More...
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string | vg::get_or_make_variant_id (const vcflib::Variant &variant) |
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string | vg::make_variant_id (const vcflib::Variant &variant) |
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void | vg::create_ref_allele (vcflib::Variant &variant, const std::string &allele) |
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int | vg::add_alt_allele (vcflib::Variant &variant, const std::string &allele) |
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template<template< class T, class A=std::allocator< T >> class Container, typename Input , typename Output > |
Container< Output > | vg::map_over (const Container< Input > &in, const std::function< Output(const Input &)> &lambda) |
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template<template< class T, class A=std::allocator< T >> class Container, typename Item > |
Container< const Item * > | vg::pointerfy (const Container< Item > &in) |
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vector< size_t > | vg::range_vector (size_t begin, size_t end) |
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vector< size_t > | vg::range_vector (size_t end) |
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size_t | vg::integer_power (size_t x, size_t power) |
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double | vg::slope (const std::vector< double > &x, const std::vector< double > &y) |
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double | vg::fit_zipf (const vector< double > &y) |
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size_t | vg::integer_power (uint64_t base, uint64_t exponent) |
| Computes base^exponent in log(exponent) time. More...
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size_t | vg::modular_exponent (uint64_t base, uint64_t exponent, uint64_t modulus) |
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string | vg::random_sequence (size_t length) |
| Returns a uniformly random DNA sequence of the given length. More...
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string | vg::percent_url_encode (const string &seq) |
| Escape "%" to "%25". More...
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string | vg::replace_in_string (string subject, const string &search, const string &replace) |
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template<class RandomIt > |
void | vg::deterministic_shuffle (RandomIt begin, RandomIt end, const uint32_t &seed) |
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template<class RandomIt > |
void | vg::deterministic_shuffle (RandomIt begin, RandomIt end, const string &seed) |
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string | vg::make_shuffle_seed (const Alignment &aln) |
| Make seeds for Alignments based on their sequences. More...
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string | vg::make_shuffle_seed (const Alignment *aln) |
| Make seeds for Alignments based on their sequences. More...
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string | vg::make_shuffle_seed (const pair< Alignment, Alignment > *alns) |
| Make seeds for pairs of Alignments based on their concatenated sequences. More...
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template<class RandomIt > |
void | vg::deterministic_shuffle (RandomIt begin, RandomIt end) |
| Do a deterministic shuffle with automatic seed determination. More...
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template<class RandomIt , class Compare , class MakeSeed > |
void | vg::sort_shuffling_ties (RandomIt begin, RandomIt end, Compare comp, MakeSeed seed) |
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template<class RandomIt , class Compare > |
void | vg::sort_shuffling_ties (RandomIt begin, RandomIt end, Compare comp) |
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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...
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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...
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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...
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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...
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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...
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void | vg::get_input_file (int &optind, int argc, char **argv, function< void(istream &)> callback) |
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string | vg::get_input_file_name (int &optind, int argc, char **argv) |
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string | vg::get_output_file_name (int &optind, int argc, char **argv) |
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void | vg::get_input_file (const string &file_name, function< void(istream &)> callback) |
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template<typename Result > |
Result | vg::parse (const string &arg) |
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template<typename Result > |
Result | vg::parse (const char *arg) |
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template<typename Result > |
bool | vg::parse (const string &arg, Result &dest) |
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template<typename Result > |
bool | vg::parse (const string &arg, typename enable_if< sizeof(Result)<=sizeof(long long) &&is_integral< Result >::value &&is_signed< Result >::value, Result >::type &dest) |
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template<> |
bool | vg::parse (const string &arg, double &dest) |
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template<> |
bool | vg::parse (const string &arg, std::regex &dest) |
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