#include <iostream>

#include <string>

#include <cstdlib>

​

int main(void) {

std::string command_string;

std::string str_row;

std::string chr_colon;

std::string period = ".";

/*

Here are the current values of file_name, chr, lookup_locus, and row, though these objects are actually defined as part of a for-loop as it reads through a "lookup table" with chromosomes and loci and a "sam file" designated by "file_name"

*/

std::string file_name = "Polly_SRR6511974.bam";

std::string chr = "ScyDAA6_1_HRSCAF_23";

int row = 0;

std::string lookup_locus = "67748";

/* 

Create a string telling the system what to do with the bam file. Intention is to construct a string saying 

"samtools view SRR6511974.bam -o lookup0_Polly_SRR6511974.sam ScyDAA6_1_HRSCAF_23:67748-67748 Polly_SRR6511974.bam"

*/

            command_string = "samtools view ";

            command_string.append(file_name);

            command_string.append(" -o lookup");

            str_row = std::__cxx11::to_string(row);

            command_string.append(str_row); 

// You want to add row1 to the string to differentiate between files generated from other LOOKUP rows

            command_string.append("_");

/* 

The file name has both accession number and ".bam" designation. You want the output to be in sam format, so just enter the accession number then a ".sam" string.

*/

            command_string.append(file_name.substr(0, file_name.find(period)));

            command_string.append(".sam ");

            chr_colon = chr.append(":");

            command_string.append(chr_colon);

            command_string.append(lookup_locus);

            command_string.append("-");

            command_string.append(lookup_locus);

            std::cout << "Outputting the following command to the console:\n" << command_string << "\n\n";

// Convert command string to const char* type so it can be outputted to console

            const char * char_command = command_string.c_str();

// From each sample file, extract the reads within 100bp of the current row in the lookup table.

            system(char_command);

}