Bcf2pro_file Class Reference

Because of the god awful mess that are vcf header lines. More...

#include <bcf2pro_file.h>

Inheritance diagram for Bcf2pro_file:

Collaboration diagram for Bcf2pro_file:

Public Member Functions
	Bcf2pro_file (bool call)
void	set_mpileup (const int &, const int &)
Locus	read_header_profile (void)
	< Writes a file header. More...
Locus	read_header (void)
	Reads a file header.
Public Member Functions inherited from Indexed_file< Locus >
void	set_index (const File_index &)
	Sets the File_index.
File_index	get_index (void) const
	Returns the File_index.
Indexed_file &	write (const Locus &)
	Returns the position in the file. More...
Indexed_file &	read (Locus &)
id1_t	get_pos (const Locus &) const
void	write_header (const Locus &)
	Writes a file header.
Locus	read_header (void)
	Reads a file header.
Public Member Functions inherited from Data_file< Locus >
void	open (const char *, const std::ios_base::openmode &)
	! The function that opens a Data_file (if file).
void	open_extention (const char *, const std::ios_base::openmode &)
	! Doesn't check extension.
void	open_from (Base_file &)
	! Appends to a file. More...
void	open_header (Base_file &)
	Opens a header for a Flat_file. More...
Data_file &	write (const Locus &)
	Writes a row to the file and advances one row. More...
Data_file &	read (Locus &)
	Reads a row from the file and advances one row. More...
Public Member Functions inherited from Base_file
const std::fstream::openmode &	openmode ()
	returns the open mode.
const std::string &	filename ()
	returns the filename.
	Base_file ()
	returns the concatenated flag. More...
void	open_no_extention (const char *, const std::ios::openmode &)
	The function that opens a indexed_file (if file).
void	open (const std::ios::openmode &)
	Opens a Base_file to the cin/cout.
void	open (std::iostream *, const std::ios_base::openmode &)
	Opens a Base_file to an istream.
void	open (std::istream *, const std::ios_base::openmode &)
	Opens a Base_file to an istream.
void	open (std::ostream *, const std::ios_base::openmode &)
	Opens a Base_file to an istream.
std::istream *	get_in (void)
	returns the istream.
std::ostream *	get_out (void)
	returns the ostream.
void	close (void)
	Close iostreams, writes tail, etc.
void	close_table (void)
	Ends table w/o closing iostreams.
bool	is_open (void) const
	Returns true iff Base_file is open.
bool	table_is_open (void) const
	Returns true iff a table is open in Base_file.
bool	binary (void) const
	Returns true iff a table is open in binary mode.
Data *	read_header (void)
	Returns a pointer to a new instance of the derived data class.
void	write_header (const Data *)
void	write_header (const File_index &, const Data *)
Base_file &	read (Data *)
	Reads from the istream.
Base_file &	read (File_index &, Indexed_data *)
Base_file &	write (const Data *)
	Writes to the ostream.
Base_file &	write (File_index &, const Indexed_data *)
void	seek (const std::streampos &pos)
	sets in and out (for reading and writing) to position pos.
void	seekg (const std::streampos &pos)
	sets in (for reading) to position pos.
void	seekp (const std::streampos &pos)
	sets out (for writing) to position pos.
void	seek (std::streampos pos, std::ios_base::seekdir way)
	TODO.
void	seekg (std::streampos off, std::ios_base::seekdir way)
	TODO.
void	seekp (std::streampos off, std::ios_base::seekdir way)
	TODO.
std::streampos	tellp (void)
	Tells streampos of out (writing)
std::streampos	tellg (void)
	Tells streampos of in (reading)
void	set_delim (const char &)
	Sets the delimiter that separates columns. Only used in text mode.
const char &	get_delim (void) const
	Gets the delimiter that separates columns. Only used in text mode.
size_t	size (void) const
	Returns the number of rows in the file. More...
bool	eof (void)
bool	indexed (void) const
bool	concatenated (void)
bool	check_concatenated (void)
bool	check_compressed (void)

Private Member Functions
void	read_text (Locus &)
	Read file in text mode. DONE.
void	read_text_profile (Locus &locus)

Private Attributes
bool	profile_
	Read file in text mode. DONE.
int	columns_
int	offset_

Additional Inherited Members
Protected Member Functions inherited from Indexed_file< Locus >
void	read_text (Locus &)
	Read file in text mode. DONE.
void	write_text (const Locus &)
	Write in text mode. DONE.
void	read_binary (Locus &)
void	write_binary (const Locus &)
Protected Member Functions inherited from Data_file< Locus >
void	read_binary (Locus &)
	Read file in binary mode.
void	write_binary (const Locus &)
	Write in binary mode.
Protected Attributes inherited from Indexed_file< Locus >
File_index	file_index_
	A file_index which turns (id0, id1)->pos.
Protected Attributes inherited from Base_file
bool	open_
	indicates whether the iostream opened succesfully
bool	table_open_
	indicates whether the header has been read successfully
bool	concatenated_
	indicates whether multiple tables are included in the file
bool	compressed_
	indicates whether the input/output stream is compressed.
char	delim_column_
	The delimiter which separates columns.
bool	read_
	File is open for reading.
bool	write_
	File is open for writing.
bool	binary_
	Binary mode flag.
bool	try_binary_
	Attempt to set binary mode flag.
bool	indexed_
	Indexed mode flag.
std::istream *	in_
	All data is read from in.
std::ostream *	out_
	All data is written is written to out.
Tmp_buffer	buffer_
	a buffer which can be rewound.
std::fstream	file_
	The file to read data from.
igzstream	gzin_
	compressed istream.
ogzstream	gzout_
	compressed ostream.
std::ios::openmode	openmode_
	stores information about the mode in which the file was opened.
std::string	filename_
	The name of the file if opened.

Detailed Description

Because of the god awful mess that are vcf header lines.

This is likely to become some form of container to handle moving data into and out of rows of map file.

Member Function Documentation

Locus Bcf2pro_file::read_header_profile ( void  )

inline

< Writes a file header.

Writes a file header.

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The documentation for this class was generated from the following files:

• mapgd_0.4/data_conversion/bcf2pro_file.h
• mapgd_0.4/data_conversion/bcf2pro_file.cc