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/*
* Header file for filter_seer.cpp
* Filters significant kmers from seer
*
*/
// C++ stl includes
#include <iostream>
#include <fstream>
#include <algorithm>
#include <list>
#include <iterator>
#include <stdexcept>
#include <math.h>
// Library includes
#include <boost/program_options.hpp>
#include "significant_kmer.hpp"
// Constants
const std::string VERSION = "1.1.2";
// Structures
struct cmdOptions
{
std::string input_file, output_file, sort_field;
double maf_filter, chi_filter, p_filter, beta_filter;
bool neg_beta, substr_kmers;
};
// Function prototypes
int parseCommandLine (int argc, char *argv[], boost::program_options::variables_map& vm);
cmdOptions processCmdLine(boost::program_options::variables_map& vm);
double fractionFilter(const std::string& filter_input);
void printHelp(boost::program_options::options_description& help);
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