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#ifndef TAKANE_FASTA_FILE_HPP
#define TAKANE_FASTA_FILE_HPP
#include "utils_files.hpp"
#include "ritsuko/ritsuko.hpp"
#include <filesystem>
#include <stdexcept>
#include <string>
/**
* @file fasta_file.hpp
* @brief Validation for FASTA files.
*/
namespace takane {
/**
* @namespace takane::fasta_file
* @brief Definitions for FASTA files.
*/
namespace fasta_file {
/**
* If `Options::fasta_file_strict_check` is provided, this enables stricter checking of the FASTA file contents and indices.
* By default, we just look at the first few bytes to verify the files.
*
* @param path Path to the directory containing the FASTA 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& famap = internal_json::extract_typed_object_from_metadata(metadata.other, "fasta_file");
const std::string& vstring = internal_json::extract_string_from_typed_object(famap, "version", "fasta_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 + "'");
}
internal_files::check_sequence_type(famap, "fasta_file");
// Check if it's indexed.
bool indexed = internal_files::is_indexed(famap);
auto fpath = path / "file.fasta.";
if (indexed) {
fpath += "bgz";
} else {
fpath += "gz";
}
internal_files::check_gzip_signature(fpath);
auto reader = internal_other::open_reader<byteme::GzipFileReader>(fpath, 10);
byteme::PerByte<> pb(&reader);
if (!pb.valid() || pb.get() != '>') {
throw std::runtime_error("FASTA file does not start with '>'");
}
if (indexed) {
auto fixpath = path / "file.fasta.fai";
if (!std::filesystem::exists(fixpath)) {
throw std::runtime_error("missing FASTA index file");
}
auto ixpath = fpath;
ixpath += ".gzi";
if (!std::filesystem::exists(ixpath)) {
throw std::runtime_error("missing BGZF index file");
}
}
if (options.fasta_file_strict_check) {
options.fasta_file_strict_check(path, metadata, options, indexed);
}
}
}
}
#endif
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