A library for working with phylogenetic data.
v0.25.0
vcf_common.cpp File Reference
#include "genesis/population/formats/vcf_common.hpp"
#include <htslib/hts.h>
#include <htslib/vcf.h>
#include <cassert>
#include <cstring>
#include <stdexcept>

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Namespaces

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

Functions

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)