fastq.cc

#include <Sequence/fastq.hpp>
#include <functional>
#include <iostream>

namespace Sequence
{
    fastq::fastq(void) : Seq(), quality(std::string()), repeat_name(true) {}

    fastq::fastq(const std::string &name, const std::string &seq,
                 const std::string &qual)
        : Seq(name, seq), quality(qual), repeat_name(true)
    {
    }

    fastq::fastq(std::string &&name, std::string &&seq, std::string &&qual)
        : Seq(std::move(name), std::move(seq)), quality(std::move(qual)),
          repeat_name(true)
    {
    }

    fastq::fastq(const Seq &s)
        : Seq(s.name, s.seq), quality(std::string()), repeat_name(true)
    {
    }

    fastq::fastq(Seq &&s)
        : Seq(std::move(s)), quality(std::string()), repeat_name(true)
    {
    }

    void
    fastq::repname(const bool &b)
    {
        repeat_name = b;
    }

    std::istream &
    fastq::read(std::istream &stream)
    {
        if (stream.peek() == EOF)
            return stream;
        if (char(stream.peek()) != '@')
            throw std::runtime_error("Sequence::fastq::read - error: record "
                                     "did not begin with \'@\'");
        std::string temp;
        stream.ignore(1, '@');
        std::getline(stream, name);
        std::getline(stream, seq);
        stream >> std::ws;
        if (char(stream.peek()) != '+')
            throw std::runtime_error("Sequence::fastq::read - error: third "
                                     "line did not begin with \'+\'");
        stream >> temp >> std::ws;
        if (temp.size() == 1)
            repeat_name = false;
        quality.resize(seq.length());
        stream.read(&quality[0], std::streamsize(seq.length()));
        stream >> std::ws;
        if (seq.length() != quality.length())
            throw std::runtime_error("Sequence::fastq::read - error: sequence "
                                     "and quality strings differ in length");
        return stream;
    }

    std::ostream &
    fastq::print(std::ostream &stream) const
    {
        stream << '@' << name << '\n' << seq << '\n' << '+';
        if (this->repeat_name)
            {
                stream << name;
            }
        stream << '\n' << quality;
        return stream;
    }
} //ns Sequence