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
|
#ifndef _ASSEMBLY_COUNTERS_H_
#define _ASSEMBLY_COUNTERS_H_
#include "Common/IOUtil.h"
#include <iostream>
#include <cassert>
#include <string>
namespace BloomDBG {
/**
* Counters for tracking assembly statistics and producing
* progress messages.
*/
struct AssemblyCounters
{
/** reads consisting entirely of solid k-mers */
size_t solidReads;
/**
* reads consisting entirely of k-mers already
* included in output contigs
*/
size_t visitedReads;
size_t readsProcessed;
size_t basesAssembled;
size_t contigID;
AssemblyCounters() : solidReads(0), visitedReads(0),
readsProcessed(0), basesAssembled(0), contigID(0) {}
/** serialize counters as a TSV table */
friend std::ostream& operator<<(std::ostream& out,
const AssemblyCounters& o)
{
/* write headers */
out << "solid_reads"
<< '\t' << "processed_reads"
<< '\t' << "bases_assembled"
<< '\t' << "next_contig_id"
<< '\n';
/* write data */
out << o.solidReads
<< '\t' << o.readsProcessed
<< '\t' << o.basesAssembled
<< '\t' << o.contigID
<< '\n';
return out;
}
/** deserialize counters from a TSV table */
friend std::istream& operator>>(std::istream& in,
AssemblyCounters& o)
{
/* ignore header line */
std::string headers;
getline(in, headers);
/* read data */
in >> o.solidReads
>> expect("\t") >> o.readsProcessed
>> expect("\t") >> o.basesAssembled
>> expect("\t") >> o.contigID
>> expect("\n");
return in;
}
};
} /* end of BloomDBG namespace */
#endif
|
