Variant Class Reference

Class for a single variant. More...

#include <ppvcf.hpp>

Public Member Functions
	Variant (const uint32_t _nsamples)
	~Variant ()
void	update_till_info (bcf_hdr_t *header, bcf1_t *record)
void	add_genotype (const uint8_t a1, const uint8_t a2, const bool phased)
string	get_seqname () const
int	get_pos () const
string	get_idx () const
string	get_ref () const
vector< string >	get_alts () const
string	get_alt (const int i) const
string	get_quality () const
string	get_info (const string &k) const

Private Member Functions
void	store_filter (bcf_hdr_t *header, bcf1_t *record)
void	store_info (bcf_hdr_t *header, bcf1_t *record)

Private Attributes
string	seq_name
	Chromosome.
int	pos
	Position (0-based)
string	idx
	Identifier.
string	ref
	Reference base(s)
vector< string >	alts
	Alternate base(s)
string	quality
	Phred-scaled quality score.
string	filter
	Filter status.
map< string, string >	info
	Additional information.
uint32_t	nsamples
	Total number of samples.
uint32_t	gti
	Genotype counter represeting how many GTs have been stored.
vector< GT >	genotypes
	Genotype fields.

Detailed Description

Class for a single variant.

Single line extracted from a VCF file.

Constructor & Destructor Documentation

Variant()

Variant::Variant ( const uint32_t  _nsamples )

inline

Constructor

Parameters

_nsamples

is the number of samples

~Variant()

Variant::~Variant ( )

inline

Destructor

Member Function Documentation

add_genotype()

void Variant::add_genotype ( const uint8_t  a1, const uint8_t  a2, const bool  phased  )

inline

Store a single genotype information.

Parameters

a1	is the first allele
a2	is the second allele
phased	is true if the genotype is phased, false otherwise

get_alt()

string Variant::get_alt ( const int  i ) const

inline

Returns

the i-th (1-based) alternate allele

get_alts()

vector<string> Variant::get_alts ( ) const

inline

Returns

the alternate alleles

get_idx()

string Variant::get_idx ( ) const

inline

Returns

the variant identifier

get_info()

string Variant::get_info ( const string &  k ) const

inline

Extract the information value associated to a key.

Parameters

k	is the key

Returns

the value associated to key k

get_pos()

int Variant::get_pos ( ) const

inline

Returns

the (0-based) position of the variant

get_quality()

string Variant::get_quality ( ) const

inline

Returns

the variant quality

get_ref()

string Variant::get_ref ( ) const

inline

Returns

the reference allele

get_seqname()

string Variant::get_seqname ( ) const

inline

Returns

the chromosome of the variant

store_filter()

void Variant::store_filter ( bcf_hdr_t *  header, bcf1_t *  record  )

inlineprivate

Extract the filter field from record and store it as a string.

Parameters

header	is the htslib header
record	is a htslib record

store_info()

void Variant::store_info ( bcf_hdr_t *  header, bcf1_t *  record  )

inlineprivate

Extract the additional information from record and store them as a map<string, string>.

Parameters

header	is the htslib header
record	is a htslib record

update_till_info()

void Variant::update_till_info ( bcf_hdr_t *  header, bcf1_t *  record  )

inline

Extract and store the first 8 fields of record.

Parameters

header	is the htslib header
record	is a htslib record

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

• ppvcf.hpp