VCF Class Reference

Class for vcf file. More...

#include <ppvcf.hpp>

Public Member Functions
	VCF (char *vcf_path, const int n_threads_, const int block_size_)
	~VCF ()
bool	parse ()
vector< Variant >	get_variants () const

Private Member Functions
char *	get_samples (char *const fmt_line, const size_t len)
tuple< uint8_t, uint8_t, bool >	extract_genotype (char *start)
void	fill_variant (const uint32_t var_idx)
void	fill_genotypes ()

Private Attributes
htsFile *	vcf
	htslib file
bcf_hdr_t *	vcf_header
	htslib header
bcf1_t *	vcf_record
	htslib record
int	n_samples
	Total number of samples per variant.
vector< Variant >	variants
	Variants read.
vector< str_w_l >	fmt_lines
	Genotype fields as cstring (from "GT" to the end of each line)
size_t	block_size
	Number of variants to read at each iteration.
size_t	to_parse
	Number of variants read in the last iteration.
int	n_threads
	Number of threads to use.

Detailed Description

Class for vcf file.

VCF file.

Constructor & Destructor Documentation

VCF()

VCF::VCF ( char *  vcf_path, const int  n_threads_, const int  block_size_  )

inline

Constructor

Parameters

vcf_path	is the path to the input vcf file
n_threads_	is the number of threads to use
block_size_	is the number of variants to read at each iteration

~VCF()

VCF::~VCF ( )

inline

Destructor

Member Function Documentation

extract_genotype()

tuple<uint8_t, uint8_t, bool> VCF::extract_genotype ( char *  start )

inlineprivate

Extracts information from a cstring representing a genotype

Parameters

start

is a cstring

Returns

a tuple containing the first allele, the second allele, and the phased flag

fill_genotypes()

void VCF::fill_genotypes ( )

inlineprivate

Extracts and store the genotypes of all the variants read in the last iteration

fill_variant()

void VCF::fill_variant ( const uint32_t  var_idx )

inlineprivate

Extracts and stores the genotype fields associated to the {var_idx}-th variant read in the last iteration

Parameters

var_idx

is an index

get_samples()

char* VCF::get_samples ( char *const  fmt_line, const size_t  len  )

inlineprivate

Extract the genotype information from a vcf line

Parameters

fmt_line	is a line of the input vcf file
len	is the length of fmt_line

Returns

a cstring representing the genotypes information

get_variants()

vector<Variant> VCF::get_variants ( ) const

inline

Returns

the variants read in the last iteration

parse()

bool VCF::parse ( )

inline

Parse block_size lines from the input vcf file

Returns

false if less than block_size lines have been read (due to EOF), true otherwise.

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

• ppvcf.hpp