Summary statistics from the allele command. More...

#include <allele.h>

Inheritance diagram for Allele:

Collaboration diagram for Allele:

Public Member Functions
Allele &	operator= (const Allele &)
	use the = operator to assign Allele.

	Allele (std::vector< std::string >)
	Instance of constructor required by Data, but Allele doesn't actually need the vector to initialize.

std::string	header (void) const
	returns first two lines of a file.

size_t	size (void) const
	The size of the class in bytes.

const std::string	get_file_name (void) const
	Returns the default file extension.

const std::string	get_table_name (void) const
	Returns the destination table name.

const bool	get_binary (void) const
	Returns the destination table name.

const std::string	sql_header (void) const
	Returns a string to create an SQL table.

const std::string	sql_column_names (void) const
	Returns the column names in the SQL table.

const std::string	sql_values (void) const
	Returns a string to insert values in an SQL table.

Public Member Functions inherited from Indexed_data
void	write_pos (std::ostream &str) const

void	read_pos (std::istream &str)

	Indexed_data (std::vector< std::string > &)

id1_t	get_abs_pos (void) const
	Indexed data needs to associate each datum with a position in the genome.

void	set_abs_pos (const id1_t &)
	Indexed data needs to associate each datum with a position in the genome.

const bool	indexed () const

Public Member Functions inherited from Data
void	read_binary (std::istream &str)

void	write_binary (std::ostream &str) const

	Data (std::vector< std::string > &)

virtual void	sql_read (std::istream &)
	Reads the values...

Data Fields
char	delim
	the delimiter used when reading/writing the class in text mode.

count_t	excluded
	A count of the number of samples that were excluded due to filtering criteria.

bool	pooled
	Inferred from pooled or labeled sequencing?

float_t	freq
	frequency of major allele.

gt_t	ref
	identity of ref allele.

gt_t	minor
	identity of minor allele.

gt_t	major
	identity major allele.

gt_t	e1
	identity of error1

gt_t	e2
	identity of error2.

float_t	error
	ml error rate.

float_t	null_error
	error rate assuming Major allele monomorphism.

float_t	null_error2
	error rate assuming Minor allele monomorphism.

count_t	coverage
	population coverage.

float_t	efc
	number of 'effective' chromosomes in the sample.

float_t	ll

float_t	monoll

float_t	hwell
	log likelihoods.

float_t	MM
	frequency of genotype MM in the population.

float_t	Mm
	frequency of genotype Mm in the population.

float_t	mm
	frequency of genotype mm in the population.

count_t	N
	number of individual at the site.

float_t	f
	HW statistic.

float_t	h
	heterozygosity.

float_t	gof
	gof statistic.

Static Public Attributes
static const std::string	table_name ="GENOME"
	The destination table in the database. More...

static const std::string	file_name =".map"
	Default file extension. More...

static const bool	binary =false
	Default file extension.

Static Public Attributes inherited from Data
static const std::string	file_name =".txt"
	The read function must be defined in the child class. More...

static const std::string	table_name ="NONE"
	The read function must be defined in the child class. More...

Private Member Functions
void	read (std::istream &str)
	The read function must be defined in the child class.

void	write (std::ostream &str) const
	! the write function must be ? by the child class.

Static Private Member Functions
static Data *	create (const std::vector< std::string > &Columns)

Static Private Attributes
static const Registration	registered =Registration(Allele::table_name, Allele::create)

Additional Inherited Members
Static Public Member Functions inherited from Data
static Data *	new_from_str (const std::string &, const std::vector< std::string > &)
	Constructs an instance of the class Registered w/ string.

Protected Attributes inherited from Indexed_data
id1_t	abs_pos_

Detailed Description

Summary statistics from the allele command.

Field Documentation

const std::string Allele::file_name =".map"

static

Default file extension.

The destination table in the Db.

const std::string Allele::table_name ="GENOME"

static

The destination table in the database.

The destination table in the Db.

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