A library for working with phylogenetic data.
v0.25.0
variant.cpp File Reference
#include "genesis/population/functions/variant.hpp"
#include "genesis/population/functions/base_counts.hpp"
#include "genesis/utils/io/char.hpp"
#include <htslib/hts.h>
#include <htslib/vcf.h>
#include <array>
#include <cassert>
#include <cstring>
#include <iostream>
#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

Variant convert_to_variant (SimplePileupReader::Record const &record, unsigned char min_phred_score)
 
Variant convert_to_variant (VcfRecord const &record)
 
std::array< std::pair< char, size_t >, 4 > sorted_variant_counts (Variant const &variant, bool reference_first)
 
std::ostream & to_sync (Variant const &var, std::ostream &os)
 Output a Variant instance to a stream in the PoPoolation2 sync format. More...
 
BaseCounts total_base_counts (Variant const &variant)