fastq_file.hpp

Go to the documentation of this file.

#ifndef TAKANE_FASTQ_FILE_HPP
#define TAKANE_FASTQ_FILE_HPP
 
#include "utils_files.hpp"
#include "ritsuko/ritsuko.hpp"
#include "byteme/byteme.hpp"
 
#include <filesystem>
#include <stdexcept>
#include <string>
 
namespace takane {
 
namespace fastq_file {
 
inline void validate(const std::filesystem::path& path, const ObjectMetadata& metadata, Options& options) {
    const std::string type_name = "fastq_file"; // use a separate variable to avoid dangling reference warnings from GCC.
    const auto& fqmap = internal_json::extract_typed_object_from_metadata(metadata.other, type_name);
 
    const std::string version_name = "version"; // again, avoid dangling reference warnings.
    const std::string& vstring = internal_json::extract_string_from_typed_object(fqmap, version_name, type_name);
    auto version = ritsuko::parse_version_string(vstring.c_str(), vstring.size(), /* skip_patch = */ true);
    if (version.major != 1) {
        throw std::runtime_error("unsupported version string '" + vstring + "'");
    }
 
    internal_files::check_sequence_type(fqmap, type_name.c_str());
 
    // Checking the quality type and offset.
    {
        const std::string qtype_name = "quality_type"; // again, avoid dangling reference warnings.
        const std::string& qtype = internal_json::extract_string(fqmap, qtype_name, [&](std::exception& e) -> void {
            throw std::runtime_error("failed to extract 'fastq_file." + qtype_name + "' from the object metadata; " + std::string(e.what())); 
        });
 
        if (qtype == "phred") {
            auto oIt = fqmap.find("quality_offset");
            if (oIt == fqmap.end()) {
                throw std::runtime_error("expected a 'fastq_file.quality_offset' property");
            }
 
            const auto& val = oIt->second;
            if (val->type() != millijson::NUMBER) {
                throw std::runtime_error("'fastq_file.quality_offset' property should be a JSON number");
            }
 
            double offset = reinterpret_cast<const millijson::Number*>(val.get())->value();
            if (offset != 33 && offset != 64) {
                throw std::runtime_error("'fastq_file.quality_offset' property should be either 33 or 64");
            }
        } else if (qtype != "solexa") {
            throw std::runtime_error("unknown value '" + qtype + "' for the 'fastq_file." + qtype_name + "' property");
        }
    }
 
    // Check if it's indexed.
    bool indexed = internal_files::is_indexed(fqmap);
    auto fpath = path / "file.fastq.";
    if (indexed) {
        fpath += "bgz";
    } else {
        fpath += "gz";
    }
 
    internal_files::check_gzip_signature(fpath);
    {
        auto reader = internal_other::open_reader<byteme::GzipFileReader>(fpath, byteme::GzipFileReaderOptions());
        char first_val;
        if (reader->read(reinterpret_cast<unsigned char*>(&first_val), 1) == 0 || first_val != '@') {
            throw std::runtime_error("FASTQ file does not start with '@'");
        }
    }
 
    if (indexed) {
        auto fixpath = path / "file.fastq.fai";
        if (!std::filesystem::exists(fixpath)) {
            throw std::runtime_error("missing FASTQ index file");
        }
 
        auto ixpath = fpath;
        ixpath += ".gzi";
        if (!std::filesystem::exists(ixpath)) {
            throw std::runtime_error("missing BGZF index file");
        }
    }
 
    if (options.fastq_file_strict_check) {
        options.fastq_file_strict_check(path, metadata, options, indexed);
    }
}
 
}
 
}
 
#endif