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
|
#include "QualityValueProfile.hpp"
QualityValueProfile::QualityValueProfile(int _wordSize,
int _numQualityValues) {
wordSize = _wordSize;
numQualityValues = _numQualityValues;
// Initialize the tuple metrics to map from seq->index
tm.Initialize(wordSize);
nWords = 1 << (2*wordSize);
// Initialize the matrix of quality values.
profile.Grow(nWords, numQualityValues);
profile.Initialize(0);
}
void QualityValueProfile::Update(Nucleotide *seq, QualityValue qv) {
DNATuple tuple;
if (tuple.FromStringLR(seq, tm)) {
profile.Set(tuple.tuple, qv, profile(tuple.tuple, qv) + 1);
}
}
void QualityValueProfile::Print(std::ofstream &out) {
out << wordSize << " " << numQualityValues
<< " " << CDF_GRANULARITY << std::endl;
profile.Print(out);
}
void QualityValueProfile::ProfileToCDF() {
int qv;
int wordIndex;
for (wordIndex = 0 ; wordIndex < nWords; wordIndex++) {
int totalSamples = 0;
for (qv = 0; qv < numQualityValues; qv++) {
totalSamples += profile(wordIndex, qv);
profile.Set(wordIndex, qv, totalSamples);
}
for (qv = 0; qv < numQualityValues; qv++ ){
profile.Set(wordIndex, qv, ((profile(wordIndex,qv) * 1.0) / totalSamples) * CDF_GRANULARITY);
}
}
}
|
