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 GRAPHIO_H
#define GRAPHIO_H 1
#include "Graph/Options.h"
#include "AdjIO.h"
#include "AsqgIO.h"
#include "DistIO.h"
#include "DotIO.h"
#include "FastaIO.h"
#include "GfaIO.h"
#include "SAMIO.h"
#include <cassert>
#include <cstdlib> // for abort
#include <istream>
#include <ostream>
#include <string>
/** Write the graph g to the specified output stream in the format
* specified by opt::format.
*/
template <typename Graph>
std::ostream& write_graph(std::ostream& out, const Graph& g,
const std::string& program, const std::string& commandLine)
{
switch (opt::format) {
case ADJ:
return out << adj_writer<Graph>(g);
case ASQG:
return write_asqg(out, g);
case DIST:
return write_dist(out, g);
case DOT: case DOT_MEANCOV:
return out << dot_writer(g);
case GFA1:
return write_gfa1(out, g);
case GFA2:
return write_gfa2(out, g);
case SAM:
return write_sam(out, g, program, commandLine);
default:
assert(false);
abort();
}
}
#include "ContigGraph.h"
/** Read a graph. */
template <typename Graph, typename BetterEP>
std::istream& read_graph(std::istream& in, ContigGraph<Graph>& g,
BetterEP betterEP)
{
in >> std::ws;
assert(in);
switch (in.peek()) {
case '@': // @SQ: SAM format
return read_sam_header(in, g);
case 'd': // digraph: GraphViz dot format (directed graph)
case 'g': // graph: GraphViz dot format (undirected graph)
return read_dot<Graph>(in, g, betterEP);
case 'H': {
in.get();
char c = in.peek();
in.unget();
assert(in);
switch (c) {
case 'T': // HT: ASQG format
return read_asqg(in, g);
case '\t': // H: GAF format
return read_gfa(in, g, betterEP);
default:
std::cerr << "Unknown file format: `H" << c << "'\n";
exit(EXIT_FAILURE);
}
break;
}
case '>': // FASTA format for vertices
return read_fasta(in, g);
default: // adj format
return read_adj(in, g, betterEP);
}
}
/** Disallow parallel edges. */
struct DisallowParallelEdges {
template <typename EP>
EP operator()(const EP& a, const EP& b) const
{
std::cerr << "error: parallel edges:"
" [" << a << "], [" << b << "]\n";
exit(EXIT_FAILURE);
}
};
/** Read a graph. */
template <typename Graph>
std::istream& operator>>(std::istream& in, ContigGraph<Graph>& g)
{
return read_graph(in, g, DisallowParallelEdges());
}
#endif
|
