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
|
#ifndef CONTIGPATH_H
#define CONTIGPATH_H 1
#include "ContigNode.h"
#include <algorithm>
#include <cassert>
#include <functional>
#include <istream>
#include <sstream>
#include <string>
#include <ostream>
#include <vector>
/** A sequence of ContigNode. */
typedef std::vector<ContigNode> ContigPath;
/** Reverse and complement the specified path. */
template<typename T>
void reverseComplement(T first, T last)
{
std::reverse(first, last);
for (T it = first; it < last; ++it)
if (!it->ambiguous())
*it ^= 1;
}
/** Return the reverse complement of the specified path. */
static inline ContigPath reverseComplement(const ContigPath& path)
{
ContigPath rc(path.rbegin(), path.rend());
for (ContigPath::iterator it = rc.begin(); it < rc.end(); ++it)
if (!it->ambiguous())
*it ^= 1;
return rc;
}
static inline std::ostream& operator<<(std::ostream& out,
const ContigPath& o)
{
assert(!o.empty());
ContigPath::const_iterator it = o.begin();
out << get(g_contigNames, *it);
for (++it; it != o.end(); ++it)
out << ' ' << get(g_contigNames, *it);
return out;
}
static inline std::istream& operator>>(std::istream& in,
ContigPath& o)
{
o.clear();
std::string s;
if (getline(in, s)) {
std::istringstream ss(s);
for (std::string name; ss >> name;)
o.push_back(find_vertex(name, g_contigNames));
assert(ss.eof());
}
return in;
}
static inline void markSeenInPath(std::istream& in,
std::vector<bool>& marked)
{
assert(in.good());
std::string s;
ContigPath path;
while (in >> s >> path) {
if (path.empty()) {
size_t i = get(g_contigNames, s);
assert(i < marked.size());
marked[i] = true;
}
for (ContigPath::const_iterator it = path.begin();
it != path.end(); ++it) {
if (!it->ambiguous()) {
size_t i = it->contigIndex();
assert(i < marked.size());
marked[i] = true;
}
}
}
assert(in.eof());
}
#endif
|
