vcf_common.hpp File Reference

#include <cstdint>
#include <string>
#include <vector>
#include "genesis/population/genome_locus_set.hpp"
#include "genesis/population/genome_region.hpp"
#include "genesis/population/genome_region_list.hpp"

Go to the source code of this file.

Classes
class	VcfGenotype
	Simple wrapper class for one genotype field for a sample. More...
struct	VcfSpecification
	Collect the four required keys that describe an INFO or FORMAT sub-field of VCF/BCF files. More...

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::population

Enumerations
enum	VcfHeaderLine : int {   kFilter = 0, kInfo = 1, kFormat = 2, kContig = 3,   kStructured = 4, kGeneric = 5 }
	Specification for the values determining header line types of VCF/BCF files. More...
enum	VcfValueSpecial : int {   kFixed = 0, kVariable = 1, kAllele = 2, kGenotype = 3,   kReference = 4 }
	Specification for special markers for the number of values expected for key-value-pairs of VCF/BCF files. More...
enum	VcfValueType : int { kFlag = 0, kInteger = 1, kFloat = 2, kString = 3 }
	Specification for the data type of the values expected in key-value-pairs of VCF/BCF files. More...

Functions
Variant	convert_to_variant_as_individuals (VcfRecord const &record, bool use_allelic_depth=false)
	Convert a VcfRecord to a Variant, treating each sample as an individual, and combining them all into one SampleCounts sample. More...
Variant	convert_to_variant_as_pool (VcfRecord const &record)
	Convert a VcfRecord to a Variant, treating each sample column as a pool of individuals. More...
GenomeLocusSet	genome_locus_set_from_vcf_file (std::string const &file)
	Read a VCF file, and use its positions to create a GenomeLocusSet. More...
GenomeRegionList	genome_region_list_from_vcf_file (std::string const &file)
	Read a VCF file, and use its positions to create a GenomeRegionList. More...
void	genome_region_list_from_vcf_file (std::string const &file, GenomeRegionList &target)
	Read a VCF file, and add its positions to an existing GenomeRegionList. More...
std::string	vcf_genotype_string (std::vector< VcfGenotype > const &genotypes)
	Return the VCF-like string representation of a set of VcfGenotype entries. More...
size_t	vcf_genotype_sum (std::vector< VcfGenotype > const &genotypes)
	Return the sum of genotypes for a set of VcfGenotype entries, typically used to construct a genotype matrix with entries 0,1,2. More...
std::string	vcf_hl_type_to_string (int hl_type)
	Internal helper function to convert htslib-internal BCF_HL_* header line type values to their string representation as used in the VCF header ("FILTER", "INFO", "FORMAT", etc). More...
std::string	vcf_value_special_to_string (int vl_type_num)
std::string	vcf_value_special_to_string (VcfValueSpecial vl_type_num)
std::string	vcf_value_type_to_string (int ht_type)
std::string	vcf_value_type_to_string (VcfValueType ht_type)