gafkluge Namespace Reference

Classes
struct	GafRecord
struct	GafStep

Functions
std::string	int_to_string (int64_t i)
int64_t	string_to_int (const std::string &s)
bool	is_missing (const std::string &s)
bool	is_missing (int64_t i)
bool	is_gaf_header_line (const std::string &line)
	Returns true if the given line is a GAF header line. More...
bool	is_gaf_header_line (const char *line)
void	write_gaf_file_header (std::ostream &out, const std::string &version)
	Writes a GAF file header with the given version number to the given output stream. More...
void	parse_gaf_record (const std::string &gaf_line, GafRecord &gaf_record)
void	for_each_cs (const GafRecord &gaf_record, std::function< void(const std::string &)> fn)
void	for_each_cg (const GafRecord &gaf_record, std::function< void(const char &, const size_t &)> fn)
void	for_each_cigar (const GafRecord &gaf_record, std::function< void(const char &, const size_t &, const std::string &, const std::string &)> fn)
std::ostream &	operator<< (std::ostream &os, const gafkluge::GafStep &gaf_step)
std::ostream &	operator<< (std::ostream &os, const gafkluge::GafRecord &gaf_record)

Function Documentation

for_each_cg()

void gafkluge::for_each_cg ( const GafRecord &  gaf_record, std::function< void(const char &, const size_t &)>  fn  )

inline

for_each_cigar()

void gafkluge::for_each_cigar ( const GafRecord &  gaf_record, std::function< void(const char &, const size_t &, const std::string &, const std::string &)>  fn  )

inline

for_each_cs()

void gafkluge::for_each_cs ( const GafRecord &  gaf_record, std::function< void(const std::string &)>  fn  )

inline

int_to_string()

std::string gafkluge::int_to_string ( int64_t  i )

inline

is_gaf_header_line() [1/2]

bool gafkluge::is_gaf_header_line ( const char *  line )

inline

Returns true if the given line is a GAF header line. Assumes that the pointer is valid.

is_gaf_header_line() [2/2]

bool gafkluge::is_gaf_header_line ( const std::string &  line )

inline

Returns true if the given line is a GAF header line.

is_missing() [1/2]

bool gafkluge::is_missing ( const std::string &  s )

inline

is_missing() [2/2]

bool gafkluge::is_missing ( int64_t  i )

inline

operator<<() [1/2]

std::ostream& gafkluge::operator<< ( std::ostream &  os, const gafkluge::GafRecord &  gaf_record  )

inline

Write a GAF record to a stream

operator<<() [2/2]

std::ostream& gafkluge::operator<< ( std::ostream &  os, const gafkluge::GafStep &  gaf_step  )

inline

parse_gaf_record()

void gafkluge::parse_gaf_record ( const std::string &  gaf_line, GafRecord &  gaf_record  )

inline

Parse a single GAF record

string_to_int()

int64_t gafkluge::string_to_int ( const std::string &  s )

inline

write_gaf_file_header()

void gafkluge::write_gaf_file_header ( std::ostream &  out, const std::string &  version  )

inline

Writes a GAF file header with the given version number to the given output stream.