tajima.cuh

#pragma once
#include <iostream>
#include <future>
#include <filesystem>
#include <fstream>
#include <string>
#include <vector>
#include <algorithm>
#include <cmath>
#include <thread>
#include "cuda_runtime.h"
#include "device_launch_parameters.h"

using namespace std;

class tajima
{
    /**
     * Execution of the Tajima's D function.
     * Execution of GENE mode and WINDOW mode.
     * Execution of NORMAL mode and PROMETHEUS mode.
     **/

private:
    /**
     * @param calc_Mode acts as a boolean variable to determine between GENE(FILE) mode or WINDOW mode.
     **/
    string calc_Mode = "FILE";
    /**
     * @param window_Size defines the base pair (bp) size of the query window for analysis. Used with WINDOW mode.
     **/
    int window_Size = 0;
    /**
     * @param step_Size defines the number of bps to skip to reach the next query window. Used with WINDOW mode.
     **/
    int step_Size = 0;

    /**
     * @param gene_List defines the CATE compatible GENE list file. Used with GENE mode.
     **/
    string gene_List;

    /**
     * @param input_Folder defines the path of the CATE indexed VCF folder.
     **/
    string input_Folder;
    /**
     * @param ouput_Path defines the path of the directory to which the outputs will be written to.
     **/
    string ouput_Path;
    /**
     * @param intermediate_Path defines the intermediate folder path.
     **/
    string intermediate_Path;

    /**
     * @param ploidy defines number of sets of chromosomes per individual organism.
     **/
    int ploidy;

    /**
     * @param tot_Blocks defines number of GPU blocks that are available
     **/
    int tot_Blocks;
    /**
     * @param tot_ThreadsperBlock defines number of threads that are available per GPU block.
     **/
    int tot_ThreadsperBlock;

    /**
     * ! Parameters used to configure PROMETHEUS mode.
     * These parameters are considered only when Prometheus is activated.
     **/

    /**
     * @param prometheus_Activate acts as a boolean variable and is used to activate Prometheus.
     **/
    string prometheus_Activate = "NO";
    /**
     * @param Multi_read acts as a boolean variable and is used to enable SSD based multiple reading of multiple files at once.
     **/
    string Multi_read = "NO";
    /**
     * @param number_of_genes defines the number of query regions Prometheus should handle at once.
     **/
    int number_of_genes = 0;
    /**
     * @param CPU_cores defines the number of CPU cores that are available at Prometheus's disposal.
     **/
    int CPU_cores = 0;
    /**
     * @param SNPs_per_Run defines the number of SNP sites the GPU will process at a time.
     **/
    int SNPs_per_Run = 0;

public:
    /**
     * Tajima has 4 constructor Functions.
     * They are for the 4 separate modal combinations that Tajima can be configured to. Namely:
     * 1. NORMAL - GENE MODE
     * 2. NORMAL - WINDOW MODE
     * 3. PROMETHEUS - GENE MODE
     * 4. PROMETHEUS - WINDOW MODE
     * All serve the common function of assigning passed variables to the classes' private variable.
     **/
    tajima();
    /**
     * NORMAL - GENE MODE constructor
     **/
    tajima(string gene_List, string input_Folder, string ouput_Path, int cuda_ID, string intermediate_Path, int ploidy);
    /**
     * NORMAL - WINDOW MODE constructor
     **/
    tajima(string calc_Mode, int window_Size, int step_Size, string input_Folder, string ouput_Path, int cuda_ID, int ploidy);
    /**
     * PROMETHEUS - GENE MODE constructor
     **/
    tajima(string gene_List, string input_Folder, string ouput_Path, int cuda_ID, string intermediate_Path, int ploidy, string prometheus_Activate, string Multi_read, int number_of_genes, int CPU_cores, int SNPs_per_Run);
    /**
     * PROMETHEUS - WINDOW MODE constructor
     **/
    tajima(string calc_Mode, int window_Size, int step_Size, string input_Folder, string ouput_Path, int cuda_ID, int ploidy, string prometheus_Activate, string Multi_read, int number_of_genes, int CPU_cores, int SNPs_per_Run);

    /**
     * This function is used in conjunction with the constructors to set the common private variables.
     **/
    void set_Values(string gene_List, string input_Folder, string ouput_Path, int cuda_ID, string intermediate_Path, int ploidy);

    /**
     * Execution function.
     **/
    void ingress();

    /**
     * This is the normal WINDOW FUNCTION. Where there is a fixed step size.
     **/
    void window(string output_File, float a1, float e1, float e2, int N, long int combinations, vector<pair<string, string>> &folder_Index);
    /**
     * This is the sliding WINDOW FUNCTION. Where there is a not a fixed step size. But the WINDOW slides from one SNP to the next in the VCF file.
     * This is activated by setting the step_Size to 0.
     **/
    void window_Sliding(string output_File, float a1, float e1, float e2, int N, long int combinations, vector<pair<string, string>> &folder_Index);

    // vector<string> get_Countries();
    // vector<pair<string, string>> index_Folder(string &country);

    // vector<string> compound_interpolationSearch(vector<pair<string, string>> &folder_Index, int &start_Co, int &end_Co);
    // vector<int> forward_Search(int pos, vector<pair<string, string>> folder_Index, int start_Co, int end_Co);
    // vector<int> backward_Search(int pos, vector<pair<string, string>> folder_Index, int start_Co, int end_Co);

    // int getN_Split(string file);

    /**
     * This function is used to calculate the prerequisites using the sample size required for calculating Tajima's D.
     **/
    void calc_Pre(int &N_tot, float &a1, float &e1, float &e2); // calc a1 to e2

    // int calc_Pairwise(string &line, int pair_Count);

    // void split(vector<string> &line_Data, string line, string delim);
    // void split_Convert(int *line_temp, string line, string delim);
    // void split_getPos(vector<string> &line_Data, string line, string delim);
    // long int fact_half(int count);
    // long int combos_N(int count);
    // void createFile(string path, string text);
    // void createFile(string path);
};