Inheritance diagram for Vcf_data:

Collaboration diagram for Vcf_data:

Public Member Functions
	Vcf_data ()
	number of individuals sapmled

void	set_header (const File_index &, const std::vector< std::string > &)

void	put (const Data *,...)
	The write function must be defined in the child class.

void	get (Data *,...) const
	The read function must be defined in the child class.

void	put (const File_index &, const Allele &, const Population &)

id1_t	get (const File_index &, Population &) const

id1_t	get (State &) const

std::vector< std::string >	get_sample_names (void) const

File_index	get_index (void) const

Data Fields
bcf1_t *	record_

bcf_hdr_t *	header_

size_t	sample_size_

std::string	id

Base	ref

std::vector< std::string >	alt

float_t	qual

bool	filter

std::vector< std::string >	info

Base	AA
	Ancestral allele.

std::vector< count_t >	AC
	Allele count in genotypes, for each ALT allele, in the same order as listed.

std::vector< float_t >	AF
	Allele frequency for each ALT allele in the same order as listed:

count_t	AN
	Total number of alleles in called genotypes.

float_t	BQ
	RMS base quality at this position.

bool	DB
	Cigar string describing how to align an alternate allele to the reference allele. More...

count_t	DP
	Combined depth across samples, e.g. DP=154.

id1_t	END
	End position of the variant described in this record (esp. for CNVs)

bool	H2
	Membership in hapmap2.

float_t	MQ
	RMS mapping quality, e.g. MQ=52.

count_t	MQ0
	Number of MAPQ == 0 reads covering this record.

count_t	NS
	Number of samples with data.

float_t	SB
	Strand bias at this position.

bool	SOMATIC
	Indicates that the record is a somatic mutation, for cancer genomics.

bool	VALIDATED
	Validated by follow-up experiment.

Field Documentation

bool Vcf_data::DB

Cigar string describing how to align an alternate allele to the reference allele.

dbSNP membership

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

Public Member Functions