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#ifndef TAKANE_BAM_FILE_HPP
#define TAKANE_BAM_FILE_HPP
#include "utils_files.hpp"
#include "ritsuko/ritsuko.hpp"
#include <filesystem>
#include <stdexcept>
#include <string>
/**
* @file bam_file.hpp
* @brief Validation for BAM files.
*/
namespace takane {
/**
* @namespace takane::bam_file
* @brief Definitions for BAM files.
*/
namespace bam_file {
/**
* If `Options::bam_file_strict_check` is provided, it is used to perform stricter checking of the BAM file contents and indices.
* By default, 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 BAM 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 std::string& vstring = internal_json::extract_version_for_type(metadata.other, "bam_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 + "'");
}
// Magic numbers taken from https://samtools.github.io/hts-specs/SAMv1.pdf
auto ipath = path / "file.bam";
internal_files::check_gzip_signature(ipath);
internal_files::check_signature<byteme::GzipFileReader>(ipath, "BAM\1", 4, "BAM");
auto ixpath = ipath;
ixpath += ".bai";
if (std::filesystem::exists(ixpath)) {
internal_files::check_signature(ixpath, "BAI\1", 4, "BAM index");
}
// Magic number taken from https://samtools.github.io/hts-specs/CSIv1.pdf
ixpath = ipath;
ixpath += ".csi";
if (std::filesystem::exists(ixpath)) {
internal_files::check_gzip_signature(ixpath);
internal_files::check_signature<byteme::GzipFileReader>(ixpath, "CSI\1", 4, "CSI index");
}
if (options.bam_file_strict_check) {
options.bam_file_strict_check(path, metadata, options);
}
}
}
}
#endif
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