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//! [read]
#include <string> // for std::string
#include <vector> // for std::vector
#include <seqan3/alphabet/nucleotide/dna5.hpp> // for dna5 datastrucutre
#include <seqan3/argument_parser/all.hpp> // for argument_parser
#include <seqan3/core/debug_stream.hpp> // for debug_stream
#include <seqan3/io/sequence_file/input.hpp> // for sequence_file_input
int main(int argc, char * argv[])
{
// Receive the filename as program argument.
std::string filename{};
seqan3::argument_parser parser("My-first-program", argc, argv);
parser.add_positional_option(filename, "The filename of the file to read.");
try
{
parser.parse();
}
catch (seqan3::argument_parser_error const & ext)
{
seqan3::debug_stream << "[PARSER ERROR] " << ext.what() << '\n';
return 0;
}
seqan3::debug_stream << "Reading file " << filename << "\n";
// Create the vector to store sequences of type seqan3::dna5_vector.
std::vector<seqan3::dna5_vector> sequences;
// Iterate through the file and store the sequences.
seqan3::sequence_file_input file_in{filename};
for (auto & [ seq, id, qual ] : file_in)
{
sequences.push_back(seq);
}
seqan3::debug_stream << sequences << '\n';
return 0;
}
//! [read]
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