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
|
#ifndef __TEXT_BOOTSTRAP_WRITER_HPP__
#define __TEXT_BOOTSTRAP_WRITER_HPP__
#include <fstream>
#include <memory>
#include <mutex>
#include <vector>
#include "BootstrapWriter.hpp"
#include "SalmonSpinLock.hpp"
#include "Transcript.hpp"
#include "spdlog/spdlog.h"
class TextBootstrapWriter : public BootstrapWriter {
public:
TextBootstrapWriter(boost::filesystem::path& outputPath,
std::shared_ptr<spdlog::logger> logger)
: outputPath_(outputPath), logger_(logger) {
// Create the directory if it doesn't exist
if (!boost::filesystem::exists(outputPath_.parent_path())) {
boost::filesystem::create_directories(outputPath_);
}
// open the file
ofile_.open(outputPath.string());
}
~TextBootstrapWriter() {
#if defined __APPLE__
spin_lock::scoped_lock sl(writeMutex_);
#else
std::lock_guard<std::mutex> lock(writeMutex_);
#endif
ofile_.close();
}
bool writeHeader(std::string& comments,
std::vector<Transcript>& transcripts) override {
#if defined __APPLE__
spin_lock::scoped_lock sl(writeMutex_);
#else
std::lock_guard<std::mutex> lock(writeMutex_);
#endif
ofile_ << comments;
size_t numTxps = transcripts.size();
if (numTxps == 0) {
return false;
}
for (size_t tn = 0; tn < numTxps; ++tn) {
auto& t = transcripts[tn];
ofile_ << t.RefName;
if (tn < numTxps - 1) {
ofile_ << '\t';
}
}
ofile_ << '\n';
/*
for (size_t tn = 0; tn < numTxps; ++tn) {
auto& t = transcripts[tn];
ofile_ << t.EffectiveLength;
if (tn < numTxps - 1) {
ofile_ << '\t';
}
}
ofile_ << '\n';
*/
return true;
}
bool writeBootstrap(std::vector<double>& abund) override {
#if defined __APPLE__
spin_lock::scoped_lock sl(writeMutex_);
#else
std::lock_guard<std::mutex> lock(writeMutex_);
#endif
size_t numTxps = abund.size();
for (size_t tn = 0; tn < numTxps; ++tn) {
auto& a = abund[tn];
ofile_ << a;
if (tn < numTxps - 1) {
ofile_ << '\t';
}
}
ofile_ << '\n';
logger_->info("wrote {} bootstraps", numWritten_.load() + 1);
++numWritten_;
return true;
}
private:
boost::filesystem::path outputPath_;
std::ofstream ofile_;
std::shared_ptr<spdlog::logger> logger_;
// only one writer thread at a time
#if defined __APPLE__
spin_lock writeMutex_;
#else
std::mutex writeMutex_;
#endif
std::atomic<uint32_t> numWritten_{0};
};
#endif // __TEXT_BOOTSTRAP_WRITER_HPP__
|
