/*

* core_functions.h

*

* Created on: Feb 4, 2015

* Author: xinping

*/

#include <map>

#include <queue>

#include <array>

#include <climits>

#include "multi_seq_obj.h"

#ifndef CORE_FUNCTIONS_H_

#define CORE_FUNCTIONS_H_

#define MAX_NUM 1000000000000

#define MIN_NUM 0

typedef struct FORSIMPLE

{

bool debug;

int type;

int bp;

int mp;

int min;

int max;

int thread;

int one_circle_limit;

int start_position;

unsigned int max_count;

unsigned int sample_count;

float ratio_nchar;

float ratio_del;

float step;

float eps;

float p_snp;

float result_filter;

float end_condition;

} Parameters;

extern Parameters params;

using namespace std;

int printhelp();

void output_header(ofstream &out);

int Get_Name_List(const string &listname, vector<string> &infilename);

int String_Split(const string &buffer, array<string, 7> &obj, int n);

int calculate_values(double end);

int calculate_values(double end, int thread);

int new_read(ifstream &in, queue<string> &buffer, int len);

int min_last_element(vector<queue<string>> &buffer_queue);

void data_checkin(queue<string> &buffer, vector<unsigned int> &count_vector, long checkin_limit, int sample);

unsigned int position_reduce();

void output_values(ofstream &out);

void core_calculate(ifstream* ifstream_array, vector<queue<string>> &buffer_queue, ofstream &output_file);

void calculate_preprocess(const vector<string> &infilename, string &outfilename);

void test();

#endif /* CORE_FUNCTIONS_H_ */