genie-sys 0.1.1

A rust binding for `Genie` (A Open Source MPEG-G Codec).
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
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178

#include "lib.h"
#include <fstream>
#include <iostream>
#include <string>
#include "genie/format/fasta/exporter.h"
#include "genie/format/fastq/exporter.h"
#include "genie/format/fastq/importer.h"
#include "genie/format/mgrec/exporter.h"
#include "genie/format/mgrec/importer.h"
#include "genie/module/default-setup.h"
#include "genie/util/make-unique.h"

namespace geniesys {

std::string file_extension(const std::string& path) {
    auto pos = path.find_last_of('.');
    std::string ext = path.substr(pos + 1);
    for (auto& c : ext) {
        c = static_cast<char>(std::tolower(c));
    }
    return ext;
}

void convert_fastq(rust::String input_file, rust::String output_file, size_t threads) {
    UTILS_DIE_IF(input_file.empty(), "input_file must be non-empty!");
    UTILS_DIE_IF(output_file.empty(), "output_file must be non-empty!");

    std::string file1(input_file.c_str());
    std::string file2(output_file.c_str());
    std::unique_ptr<std::ifstream> file1_ptr;
    std::unique_ptr<std::ofstream> file2_ptr;
    std::istream* s1 = &std::cin;
    std::ostream* o1 = &std::cout;
    auto flow = genie::module::buildDefaultConverter(threads);

#ifdef DEBUG
    std::cout << "pwd: " << std::filesystem::current_path() << std::endl;
    std::cout << "input_file: " << file1 << std::endl;
    std::cout << "output_file: " << file2 << std::endl;
#endif

    if (file1.substr(0, 2) != "-.") {
        file1_ptr = genie::util::make_unique<std::ifstream>(file1, std::ifstream::in);
        UTILS_DIE_IF(file1_ptr->fail(), "Failed to open input_file!");
        s1 = file1_ptr.get();
    }

    if (file2.substr(0, 2) != "-.") {
        file2_ptr = genie::util::make_unique<std::ofstream>(file2, std::ofstream::binary | std::ofstream::app);
        UTILS_DIE_IF(file2_ptr->fail(), "Failed to open output_file!");
        o1 = file2_ptr.get();
    }

    flow->addImporter(genie::util::make_unique<genie::format::fastq::Importer>(BLOCKSIZE, *s1));
    flow->addExporter(genie::util::make_unique<genie::format::mgrec::Exporter>(*o1));
    flow->run();

    if (file1_ptr) file1_ptr->close();
    if (file2_ptr) file2_ptr->close();
};

void convert_fastq(rust::String input_file, rust::String sup_file, rust::String output_file, size_t threads) {
    UTILS_DIE_IF(input_file.empty(), "input_file must be non-empty!");
    UTILS_DIE_IF(sup_file.empty(), "sup_file must be non-empty!");
    UTILS_DIE_IF(output_file.empty(), "output_file must be non-empty!");

    std::string file1 = input_file.c_str();
    std::string file2 = sup_file.c_str();
    std::string file3 = output_file.c_str();
    std::unique_ptr<std::ifstream> file1_ptr;
    std::unique_ptr<std::ifstream> file2_ptr;
    std::unique_ptr<std::ofstream> file3_ptr;
    std::istream* s1 = &std::cin;
    std::ostream* o1 = &std::cout;
    auto flow = genie::module::buildDefaultConverter(threads);

#ifdef DEBUG
    std::cout << "pwd: " << std::filesystem::current_path() << std::endl;
    std::cout << "input_file: " << file1 << std::endl;
    std::cout << "sup_file: " << file2 << std::endl;
    std::cout << "output_file: " << file3 << std::endl;
#endif

    if (file1.substr(0, 2) != "-.") {
        file1_ptr = genie::util::make_unique<std::ifstream>(file1);
        UTILS_DIE_IF(file1_ptr->fail(), "Failed to open input_file!");
        s1 = file1_ptr.get();
    }

    if (file2.substr(0, 2) != "-.") {
        file2_ptr = genie::util::make_unique<std::ifstream>(file2);
        UTILS_DIE_IF(file2_ptr->fail(), "Failed to open sup_file!");
    } else {
        UTILS_DIE("Cannot use stdout as sup_file!");
    }

    if (file3.substr(0, 2) != "-.") {
        file3_ptr = genie::util::make_unique<std::ofstream>(file3, std::ofstream::binary | std::ofstream::app);
        UTILS_DIE_IF(file3_ptr->fail(), "Failed to open output_file!");
        o1 = file3_ptr.get();
    }

    flow->addImporter(genie::util::make_unique<genie::format::fastq::Importer>(BLOCKSIZE, *s1, *file2_ptr.get()));
    flow->addExporter(genie::util::make_unique<genie::format::mgrec::Exporter>(*o1));
    flow->run();

    if (file1_ptr) file1_ptr->close();
    if (file2_ptr) file2_ptr->close();
    if (file3_ptr) file3_ptr->close();
};

void convert_mgrec(rust::String input_file, rust::String output_file1, rust::String output_file2, size_t threads) {
    UTILS_DIE_IF(input_file.empty(), "input_file must be non-empty!");
    UTILS_DIE_IF(output_file1.empty(), "output_file1 must be non-empty!");

    std::string file1 = input_file.c_str();
    std::string file2 = output_file1.c_str();
    std::string file3 = output_file2.c_str();
    std::string tmp_file = file1 + ".unsupported.mgrec";
    std::unique_ptr<std::ifstream> file1_ptr;
    std::unique_ptr<std::ofstream> file2_ptr;
    std::unique_ptr<std::ofstream> file3_ptr;
    std::unique_ptr<std::ofstream> file4_ptr;
    std::istream* s1 = &std::cin;
    std::ostream* o1 = &std::cout;
    std::ostream* o2 = &std::cout;
    std::ostream* o3 = &std::cout;
    auto flow = genie::module::buildDefaultConverter(threads);

#ifdef DEBUG
    std::cout << "pwd: " << std::filesystem::current_path() << std::endl;
    std::cout << "input_file: " << file1 << std::endl;
    std::cout << "output_file: " << file2 << std::endl;
    std::cout << "output_file1: " << file3 << std::endl;
#endif

    if (file1.substr(0, 2) != ".-") {
        file1_ptr = genie::util::make_unique<std::ifstream>(file1, std::ifstream::binary);
        file4_ptr = genie::util::make_unique<std::ofstream>(tmp_file);
        UTILS_DIE_IF(file1_ptr->fail(), "Failed to open input_file!");
        UTILS_DIE_IF(file4_ptr->fail(), "Failed to open tmp_file!");
        s1 = file1_ptr.get();
        o3 = file4_ptr.get();
    }

    if (file2.substr(0, 2) != ".-") {
        file2_ptr = genie::util::make_unique<std::ofstream>(file2, std::ofstream::app);
        UTILS_DIE_IF(file2_ptr->fail(), "Failed to open output_file!");
        o1 = file2_ptr.get();
    }

    if (!file3.empty() && file3.substr(0, 2) != ".-") {
        file3_ptr = genie::util::make_unique<std::ofstream>(file3, std::ofstream::app);
        UTILS_DIE_IF(file3_ptr->fail(), "Failed to open output_file1!");
        o2 = file3_ptr.get();
    }

    flow->addImporter(genie::util::make_unique<genie::format::mgrec::Importer>(BLOCKSIZE, *s1, *o3, true));

    if (file_extension(file2) == "fastq") {
        if (file_extension(file3) == "fastq") {
            flow->addExporter(genie::util::make_unique<genie::format::fastq::Exporter>(*o1, *o2));
        } else {
            flow->addExporter(genie::util::make_unique<genie::format::fastq::Exporter>(*o1));
        }
    } else if (file_extension(file2) == "fasta") {
        flow->addExporter(genie::util::make_unique<genie::format::fasta::Exporter>(&flow->getRefMgr(), o1, threads));
    }

    flow->run();

    if (file1_ptr) file1_ptr->close();
    if (file2_ptr) file2_ptr->close();
    if (file3_ptr) file3_ptr->close();
    if (file4_ptr) file4_ptr->close();
}

}  // namespace geniesys