bed_file.hpp

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#ifndef TAKANE_BED_FILE_HPP
#define TAKANE_BED_FILE_HPP
 
#include "utils_files.hpp"
 
#include "ritsuko/ritsuko.hpp"
 
#include <filesystem>
#include <stdexcept>
#include <string>
 
namespace takane {
 
namespace bed_file {
 
inline void validate(const std::filesystem::path& path, const ObjectMetadata& metadata, [[maybe_unused]] Options& options) {
    const std::string type_name = "bed_file"; // use a separate variable to avoid dangling reference warnings from GCC.
    const auto& bedmap = 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(bedmap, 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 + "'");
    }
 
    // Check if it's indexed.
    bool indexed = internal_files::is_indexed(bedmap);
    auto fpath = path / "file.bed.";
    if (indexed) {
        fpath += "bgz";
    } else {
        fpath += "gz";
    }
 
    internal_files::check_gzip_signature(fpath);
 
    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.bed_file_strict_check) {
        options.bed_file_strict_check(path, metadata, options, indexed);
    }
}
 
}
 
}
 
#endif