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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>
/**
* @file bed_file.hpp
* @brief Validation for BED files.
*/
namespace takane {
/**
* @namespace takane::bed_file
* @brief Definitions for BED files.
*/
namespace bed_file {
/**
* If `Options::bed_file_strict_check` is provided, it is used to perform stricter checking of the BED file contents and indices.
* Currently, we don't look past the magic number to verify the files as this requires a dependency on heavy-duty libraries like, e.g., HTSlib.
*
* @param path Path to the directory containing the BED 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, [[maybe_unused]] Options& options) {
const auto& bedmap = internal_json::extract_typed_object_from_metadata(metadata.other, "bed_file");
const std::string& vstring = internal_json::extract_string_from_typed_object(bedmap, "version", "bed_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 + "'");
}
// 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
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