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

#include <bcf2pro.h>

Inheritance diagram for Bcf2pro:

Collaboration diagram for Bcf2pro:

Public Member Functions
	Bcf2pro (const std::vector< std::string > &str)

	Bcf2pro (const count_t &)

Public Member Functions inherited from Locus
void	write_binary (std::ostream &out) const

void	read_binary (std::istream &in)

	Locus (const count_t &)
	Locus is initialized to abs_pos_=0, id1=0, and set to contain 0 samples.

	Locus ()
	Locus is initialized to abs_pos_=0, id1=0, and set to contain 0 samples.

	Locus (const std::vector< std::string > &)

Locus &	operator= (const Locus &)

Locus &	operator+= (const Locus &)

const Locus	operator+ (const Locus &) const

const count_t	getindex (count_t) const
	Returns the index of the alleles in order a sorted order. More...

count_t	getcoverage (count_t) const
	Returns coverage of population/individual N.

count_t	getcoverage (void) const
	Returns total coverage.

count_t	getcount (count_t) const
	Returns the count of allele in all individuals in the population.

count_t	getcount (count_t, count_t) const
	Returns the count of individual a's b'th allele.

void	swap (count_t, count_t)
	Exchange the alleles.

void	sort (count_t)
	Sort counts from most common to least common (based on population N).

void	sort (void)
	Sort counts from most common to least common (among all non-masked sites).

void	set_quartet (const quartet_t &, const count_t &)
	Sets the quartet_t array (unsorted). More...

const quartet_t &	get_quartet (const count_t &) const
	Returns the N'th quartet at the Locus. More...

quartet_t &	get_quartet (const count_t &)
	Returns the N'th quartet at the Locus. More...

count_t	maskedcount (void) const
	Returns the count of the number of individuals that are masked.

void	maskall (void)
	Mask all lines. More...

void	unmaskall (void)
	Unmask all lines. More...

void	mask (const std::vector< size_t > &)
	Mask all lines. More...

void	unmask (const std::vector< size_t > &)
	Unmask all lines. More...

void	mask_low_cov (const count_t &dp)
	Mask site with coverage stricktly lt dp;.

char	getname (const count_t &) const
	Get the nucleotide represented by the count at the N'th indexed quartet_t.

char	getname_gt (const count_t &) const
	Get the nucleotide represented by the count at the N'th indexed quartet_t, return * if the count equals the N+1 indexed quartet.

count_t	get_extraid (const size_t &) const
	Get the extraid of the Locus. Used to represent the reference call.

void	set_extraid (const count_t &, const size_t &)
	Set the extraid of the Locus. Just used to represent the reference call.

void	resize (const size_t &)
	< Set the absolute position of the Locus. More...

std::vector< quartet_t >::iterator	begin (void)

std::vector< quartet_t >::iterator	end (void)
	Return an iterator to the quartet_t s stored at this Locus. More...

std::vector< quartet_t > ::const_iterator	cbegin (void) const
	Return an iterator to the quartet_t s stored at this Locus.

std::vector< quartet_t > ::const_iterator	cend (void) const
	Return an iterator to the quartet_t s stored at this Locus.

std::vector< std::string >	get_sample_names (void) const
	names of the samples sequenced

void	set_sample_names (const std::vector< std::string > &sample_names)
	names of the samples sequenced.

std::string	header (void) const

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

const std::string	get_file_name (void) const

const std::string	get_table_name (void) const

const bool	get_binary (void) const

const std::string	sql_header (void) const
	Return the names of the columns, along with variable type.

const std::string	sql_column_names (void) const
	Return the names of the columns.

const std::string	sql_values (void) const
	Return the values to be placed in columns.

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

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 > &)

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.

Data Fields inherited from Locus
gt_t	sorted_ [5]
	an array to allow sorted access to quartets.

std::vector< quartet_t >	sample
	The five bases A/C/G/T/N;.

Base	ref

Static Public Attributes inherited from Locus
static const gt_t	default_order [5] = {0,1,2,3,4}

static const std::string	file_name =".pro"

static const std::string	table_name ="QUARTETS"

static const bool	binary =true

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...

Protected Attributes inherited from Indexed_data
id1_t	abs_pos_

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.

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

mapgd_0.4/data_conversion/bcf2pro.h

Public Member Functions

Additional Inherited Members

Detailed Description