gff_file.hpp

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#ifndef TAKANE_GFF_FILE_HPP
#define TAKANE_GFF_FILE_HPP
 
#include "utils_files.hpp"
#include "ritsuko/ritsuko.hpp"
 
#include <filesystem>
#include <stdexcept>
#include <string>
 
namespace takane {
 
namespace gff_file {
 
inline void validate(const std::filesystem::path& path, const ObjectMetadata& metadata, Options& options) {
    const std::string type_name = "gff_file"; // use a separate variable to avoid dangling reference warnings from GCC.
    const auto& gffmap = 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(gffmap, 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 + "'");
    }
 
    auto fpath = path / "file.";
    const std::string format_name = "format"; // again, avoid dangling reference warnings.
    const std::string& fstring = internal_json::extract_string_from_typed_object(gffmap, format_name, type_name);
    if (fstring == "GFF2") {
        fpath += "gff2";
    } else if (fstring == "GFF3") {
        fpath += "gff3";
    } else {
        throw std::runtime_error("unknown value '" + fstring + "' for 'gff_file.format' property");
    }
 
    // Check if it's indexed.
    bool indexed = internal_files::is_indexed(gffmap);
    fpath += ".";
    if (indexed) {
        fpath += "bgz";
    } else {
        fpath += "gz";
    }
 
    // Check magic numbers.
    internal_files::check_gzip_signature(fpath);
 
    if (fstring == "GFF3") {
        const std::string expected = "##gff-version 3";
        const size_t expected_len = expected.size();
 
        auto reader = internal_other::open_reader<byteme::GzipFileReader>(fpath, [&]{
            byteme::GzipFileReaderOptions gopt;
            gopt.buffer_size = expected_len;
            return gopt;
        }());
        byteme::PerByteSerial<char> pb(std::move(reader));
        bool okay = pb.valid();
 
        for (size_t i = 0; i < expected_len; ++i) {
            if (!okay) {
                throw std::runtime_error("incomplete GFF3 file signature for '" + fpath.string() + "'");
            }
            if (pb.get() != expected[i]) {
                throw std::runtime_error("incorrect GFF3 file signature for '" + fpath.string() + "'");
            }
            okay = pb.advance();
        }
    }
 
    if (indexed) {
        auto ixpath = fpath;
        ixpath += ".tbi";
        internal_files::check_gzip_signature(ixpath);
        internal_files::check_signature<byteme::GzipFileReader>(ixpath, "TBI\1", 4, "tabix");
    }
 
    if (options.gff_file_strict_check) {
        options.gff_file_strict_check(path, metadata, options, indexed);
    }
}
 
}
 
}
 
#endif