simple_pileup_reader.cpp File Reference

#include "genesis/population/formats/simple_pileup_reader.hpp"
#include "genesis/sequence/functions/codes.hpp"
#include "genesis/utils/io/parser.hpp"
#include "genesis/utils/io/scanner.hpp"
#include "genesis/utils/math/bitvector/helper.hpp"
#include "genesis/utils/text/char.hpp"
#include <cassert>
#include <cstdlib>
#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
void	process_pileup_correct_input_order_check_ (utils::InputStream const &it, std::string &cur_chr, size_t &cur_pos, std::string const &new_chr, size_t new_pos)
	Local helper function to remove code duplication for the correct input order check. More...
template<>
void	SimplePileupReader::process_ancestral_base_< SimplePileupReader::Sample > (utils::InputStream &input_stream, SimplePileupReader::Sample &sample) const
template<>
void	SimplePileupReader::process_quality_string_< SimplePileupReader::Sample > (utils::InputStream &input_stream, SimplePileupReader::Sample &sample) const
template<>
void	SimplePileupReader::set_sample_read_bases_< SimplePileupReader::Sample > (std::string const &read_bases, SimplePileupReader::Sample &sample) const
template<>
void	SimplePileupReader::set_sample_read_coverage_< SimplePileupReader::Sample > (size_t read_coverage, SimplePileupReader::Sample &sample) const
template<>
void	SimplePileupReader::set_target_alternative_base_< SimplePileupReader::Record > (SimplePileupReader::Record &target) const