FASTQ

Support reading and writing fastq files 🔗. All classes/functions are available in the ivio::fastq namespace.

• FASTQ
  • Record and RecordView
  • Reader
  • Examples
    • Example - Reading record by record

Record and RecordView (record, record_view)

IVio provides the datastructures ivio::fastq::record and ivio::fastq::record_view. These are the typical input/output arguments of the readers and writers. These datastructures convertible to each other.

The record_view layout

struct record_view {
    std::string_view id;
    std::string_view seq;
    std::string_view id2;
    std::string_view qual;
};

The record layout

struct record {
    std::string id;
    std::string seq;
    std::string id2;
    std::string qual;
};

Reader (reader, reader::config)

The ivio::fastq::reader accepts a ivio::fastq::reader::config object for initialization. It initializes an object that enables you to iterate over the records of a file. It is is for-range compatible, meaning it fulfills c++ concepts of range and LegacyInputIterator. When looping over a reader it returns record_view objects that are only valid until next record is being requested from the reader. To get ownership of the data, it is required to create an object of type record.

To configure the reader one must fill the ivio::fastq::reader::config struct which declares the input file and if gzip compression is expected.

struct ivio::fastq::reader::config {
    // Source: file or stream
    std::variant<std::filesystem::path, std::reference_wrapper<std::istream>> input;

    // This is only relevant if a stream is being used
    bool compressed{};
};

Overview of the member functions of ivio::fastq::reader

struct ivio::fastq::reader {
    /*...*/
    auto next() -> std::optional<record_view>; // reads the next record
    void close() const; // closes the read file
};

Examples

Example - Reading record by record

In this example a file is being opened and print to command line

#include <iostream>
#include <ivio/ivio.h>

int main(int /*argc*/, char** argv) {
    auto inputFile = std::filesystem::path{argv[1]};
    auto reader = ivio::fastq::reader{{.input = inputFile}};
    for (auto record_view : reader) {
        std::cout << "id: "   << record_view.id << "\n";
        std::cout << "seq: "  << record_view.seq << "\n";
        std::cout << "id2: "  << record_view.id2 << "\n";
        std::cout << "qual: " << record_view.qual << "\n";

    }
}

Output

id: Seq1
seq: ACGT
id2: 
qual: !!!!
id: Seq2
seq: NNNN
id2: 
qual: !!!!