utils.h File Reference

#include <string>
#include <memory>
#include <vector>
#include <sstream>
#include "htslib/vcf.h"

Go to the source code of this file.

Namespaces
	gamgee
	gamgee::utils
	utility functions for the gamgee library

Functions
std::string	gamgee::utils::reverse_complement (const std::string &sequence)
	calculates the reverse complement of a sequence More...
std::string	gamgee::utils::complement (const std::string &sequence)
	calculates the complement of a sequence More...
std::string	gamgee::utils::complement (std::string &sequence)
	calculates the complement of a sequence in-place More...
char	gamgee::utils::complement (const char base)
	calculates the complement of a base More...
std::vector< std::string >	gamgee::utils::hts_string_array_to_vector (const char *const *const string_array, const uint32_t array_size)
	converts an array of c-strings into a vector<string> More...
void	gamgee::utils::check_max_boundary (const uint32_t index, const uint32_t size, const std::string &prefix_msg)
	checks that an index is greater than or equal to size More...
void	gamgee::utils::check_max_boundary (const uint32_t index, const uint32_t size)
	checks that an index is greater than or equal to size More...
template<class TYPE >
bool	gamgee::utils::bcf_check_equal_element (const TYPE &x, const TYPE &y)
	Check whether two values from VCF fields of primitive types (for which the == operator is defined) * are equal The function template is specialized for float fields More...
template<>
bool	gamgee::utils::bcf_check_equal_element< float > (const float &x, const float &y)
	: Check whether two float values from VCF fields are equal More...
template<class TYPE >
bool	gamgee::utils::bcf_is_vector_end_value (const TYPE &value)
template<>
bool	gamgee::utils::bcf_is_vector_end_value< int32_t > (const int32_t &value)
template<>
bool	gamgee::utils::bcf_is_vector_end_value< float > (const float &value)
template<class ITER >
const uint8_t *	gamgee::utils::cache_and_advance_to_end_if_necessary (const uint8_t *current_ptr, const uint8_t *end_ptr, ITER &it)
	advances current ptr to end of the vector if the current element is bcf_*_vector_end More...