1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
|
#ifndef TAKANE_BIGWIG_FILE_HPP
#define TAKANE_BIGWIG_FILE_HPP
#include "utils_files.hpp"
#include "ritsuko/ritsuko.hpp"
#include <filesystem>
#include <stdexcept>
#include <string>
/**
* @file bigwig_file.hpp
* @brief Validation for bigWig files.
*/
namespace takane {
/**
* @namespace takane::bigwig_file
* @brief Definitions for bigWig files.
*/
namespace bigwig_file {
/**
* If `Options::bigwig_file_strict_check` is provided, it is used to perform stricter checking of the bigWig file contents.
* 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 bigWig 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, "bigwig_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://data.broadinstitute.org/igv/projects/downloads/2.1/IGVDistribution_2.1.11/src/org/broad/igv/bbfile/BBFileHeader.java,
// which seems to use the magic number to detect endianness of the file as well.
auto ipath = path / "file.bw";
std::array<unsigned char, 4> store;
internal_files::extract_signature(ipath, store.data(), store.size());
std::array<unsigned char, 4> be_magic { 0x26, 0xFC, 0x8F, 0x88 };
std::array<unsigned char, 4> le_magic { 0x88, 0x8F, 0xFC, 0x26 };
if (store != be_magic && store != le_magic) {
throw std::runtime_error("incorrect bigWig file signature for '" + ipath.string() + "'");
}
if (options.bigwig_file_strict_check) {
options.bigwig_file_strict_check(path, metadata, options);
}
}
}
}
#endif
|
