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
|
#include "FastaWriter.h"
#include "Common/Options.h"
#include <cassert>
#include <cerrno>
#include <cstdio>
#include <cstdlib>
#include <cstring> // for strerror
#include <iostream>
#include <unistd.h> // for fsync
using namespace std;
static inline void die(const string& s)
{
cerr << "error: writing to `" << s << "': "
<< strerror(errno) << endl;
exit(EXIT_FAILURE);
}
FastaWriter::FastaWriter(const char* path, bool append)
: m_path(path), m_fileHandle(fopen(path, append ? "a" : "w"))
{
if (m_fileHandle == NULL)
die(m_path);
}
FastaWriter::~FastaWriter()
{
int n = fsync(fileno(m_fileHandle));
if (n < 0)
die(m_path);
n = fclose(m_fileHandle);
if (n < 0)
die(m_path);
m_fileHandle = NULL;
}
void FastaWriter::WriteSequence(const Sequence& seq, unsigned id,
unsigned multiplicity, const string& comment)
{
assert(m_fileHandle != NULL);
const char *sep = comment.empty() ? "" : " ";
int n = opt::rank < 0
? fprintf(m_fileHandle, ">%llu %zu %u%s%s\n%s\n",
(long long unsigned)id,
seq.length(), multiplicity,
sep, comment.c_str(),
seq.c_str())
: fprintf(m_fileHandle, ">%u:%llu %zu %u%s%s\n%s\n",
opt::rank,
(long long unsigned)id,
seq.length(), multiplicity,
sep, comment.c_str(),
seq.c_str());
if (n < 0)
die(m_path);
}
void FastaWriter::WriteSequence(const Sequence& seq, unsigned long long id, const std::string& comment)
{
assert(m_fileHandle != NULL);
int n = fprintf(m_fileHandle, ">%llu %s\n%s\n", id, comment.c_str(), seq.c_str());
if (n < 0)
die(m_path);
}
void FastaWriter::WriteSequence(const Sequence& seq, const std::string& id, const std::string& comment)
{
assert(m_fileHandle != NULL);
int n = fprintf(m_fileHandle, ">%s %s\n%s\n", id.c_str(), comment.c_str(), seq.c_str());
if (n < 0)
die(m_path);
}
|
