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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>
/**
* @file gff_file.hpp
* @brief Validation for GFF files.
*/
namespace takane {
/**
* @namespace takane::gff_file
* @brief Definitions for GFF files.
*/
namespace gff_file {
/**
* If `Options::gff_file_strict_check` is provided, this enables stricter checking of the GFF file contents.
* By default, we just look at the first few bytes to verify the files.
*
* @param path Path to the directory containing the GFF file.
* @param metadata Metadata for the object, typically read from its `OBJECT` file.
* @param options Validation options.
*/
inline void validate(const std::filesystem::path& path, const ObjectMetadata& metadata, Options& options) {
const auto& gffmap = internal_json::extract_typed_object_from_metadata(metadata.other, "gff_file");
const std::string& vstring = internal_json::extract_string_from_typed_object(gffmap, "version", "gff_file");
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& fstring = internal_json::extract_string_from_typed_object(gffmap, "format", "gff_file");
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, expected_len);
byteme::PerByte<> pb(&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
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