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
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
|
#ifndef ASSEMBLY_COVERAGEALGORITHM_H
#define ASSEMBLY_COVERAGEALGORITHM_H 1
#include "Common/Histogram.h"
#include "Common/IOUtil.h"
#include "Common/Options.h" // for opt::rank
#include <fstream>
namespace AssemblyAlgorithms {
/** Return the k-mer coverage histogram. */
static inline
Histogram coverageHistogram(const SequenceCollectionHash& c)
{
typedef SequenceCollectionHash Graph;
Histogram h;
for (Graph::const_iterator it = c.begin();
it != c.end(); ++it) {
if (it->second.deleted())
continue;
h.insert(it->second.getMultiplicity());
}
return h;
}
/** Calculate a k-mer coverage threshold from the given k-mer coverage
* histogram. */
static inline
float calculateCoverageThreshold(const Histogram& h)
{
float cov = h.firstLocalMinimum();
if (opt::rank <= 0) {
if (cov == 0)
std::cout << "Unable to determine minimum k-mer coverage\n";
else
std::cout << "Minimum k-mer coverage is " << cov << std::endl;
}
for (unsigned iteration = 0; iteration < 100; iteration++) {
Histogram trimmed = h.trimLow((unsigned)roundf(cov));
if (opt::rank <= 0)
logger(1) << "Coverage: " << cov << "\t"
"Reconstruction: " << trimmed.size() << std::endl;
unsigned median = trimmed.median();
float cov1 = sqrt(median);
if (cov1 == cov) {
// The coverage threshold has converged.
if (opt::rank <= 0)
std::cout << "Using a coverage threshold of "
<< (unsigned)roundf(cov) << "...\n"
"The median k-mer coverage is " << median << "\n"
"The reconstruction is " << trimmed.size()
<< std::endl;
if (!opt::db.empty()) {
addToDb("coverageThreshold", (unsigned)roundf(cov));
addToDb("medianKcoverage", median);
addToDb("restruction", trimmed.size());
}
return cov;
}
cov = cov1;
}
if (opt::rank <= 0)
std::cerr << "warning: coverage threshold did not converge"
<< std::endl;
return 0;
}
/** Set the coverage-related parameters e and c from the given k-mer
* coverage histogram. */
static inline
void setCoverageParameters(const Histogram& h)
{
if (!opt::coverageHistPath.empty() && opt::rank <= 0) {
std::ofstream histFile(opt::coverageHistPath.c_str());
assert_good(histFile, opt::coverageHistPath);
histFile << h;
assert(histFile.good());
}
float minCov = calculateCoverageThreshold(h);
if (opt::rank <= 0) {
if (minCov == 0)
std::cout << "Unable to determine the "
"k-mer coverage threshold" << std::endl;
else
std::cout << "The k-mer coverage threshold is " << minCov
<< std::endl;
}
if (minCov < 2)
minCov = 2;
if ((int)opt::erode < 0) {
opt::erode = (unsigned)roundf(minCov);
if (opt::rank <= 0)
std::cout << "Setting parameter e (erode) to "
<< opt::erode << std::endl;
}
if ((int)opt::erodeStrand < 0) {
opt::erodeStrand = minCov <= 2 ? 0 : 1;
if (opt::rank <= 0)
std::cout << "Setting parameter E (erodeStrand) to "
<< opt::erodeStrand << std::endl;
}
if (opt::coverage < 0) {
opt::coverage = minCov;
if (opt::rank <= 0)
std::cout << "Setting parameter c (coverage) to "
<< opt::coverage << std::endl;
}
}
/** Remove all k-mers with multiplicity lower than the given threshold */
static inline
size_t applyKmerCoverageThreshold(SequenceCollectionHash& c, unsigned kc)
{
if (kc == 0)
return 0;
for (SequenceCollectionHash::iterator it = c.begin();
it != c.end(); ++it) {
if (it->second.getMultiplicity() < kc)
it->second.setFlag(SF_DELETE);
}
return c.cleanup();
}
} // namespace AssemblyAlgorithms
#endif
|
