-
Notifications
You must be signed in to change notification settings - Fork 2
/
F2_core.cpp
85 lines (65 loc) · 2.41 KB
/
F2_core.cpp
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
/*
* F2_core
* Date: Mar-15-2013
* Author : Gabriel Renaud gabriel.reno [at sign here ] gmail.com
*
*/
#include "F2_core.h"
#include "ComputeAvgCoa_core.h"
bool addCountersInd(const int refCount1,
const int altCount1,
const double freq_ind1,
const int refCount2,
const int altCount2,
const double freq_ind2,
const bool isCpG,
const bool isSitePotentialTransition,
const bool isSitePotentialDamage,
F2Result * f2res){
//cerr<<"addCountersInd "<<refCount<<" "<<altCount<<endl;
f2res->all.addAlleleCounts(refCount1,altCount1,freq_ind1,refCount2,altCount2,freq_ind2);
if(isCpG){
f2res->onlyCpg.addAlleleCounts(refCount1,altCount1,freq_ind1,refCount2,altCount2,freq_ind2);
}else{
f2res->noCpg.addAlleleCounts(refCount1,altCount1,freq_ind1,refCount2,altCount2,freq_ind2);
}
if( isSitePotentialTransition ){
f2res->transitions.addAlleleCounts(refCount1,altCount1,freq_ind1,refCount2,altCount2,freq_ind2);
}else{
f2res->transversions.addAlleleCounts(refCount1,altCount1,freq_ind1,refCount2,altCount2,freq_ind2);
}
if( !isSitePotentialDamage ){
f2res->noDamage.addAlleleCounts(refCount1,altCount1,freq_ind1,refCount2,altCount2,freq_ind2);
}//TODO check!
}
bool computeF2pair(const double freq_ind1,
const double freq_ind2,
const bool isCpG,//true if CpG
const bool isSitePotentialTransition, //true if transition
const bool isSitePotentialDamage, //true if damage
F2Result * f2res){
double f2=(freq_ind1-freq_ind2)*(freq_ind1-freq_ind2);//(f1-f2)^2
//cerr<<f3<<"\t"<<freq_condition<<"\t"<<freq_ind1<<"\t"<<freq_condition<<"\t"<<freq_ind2<<"\t"<<f3res->all.f3Sum<<endl;
f2res->all.f2Sum += f2;
//cerr<<f3<<"\t"<<freq_condition<<"\t"<<freq_ind1<<"\t"<<freq_condition<<"\t"<<freq_ind2<<"\t"<<f3res->all.f3Sum<<endl;
f2res->all.counterSites ++;
if(isCpG){
f2res->onlyCpg.f2Sum += f2;
f2res->onlyCpg.counterSites ++;
}else{
f2res->noCpg.f2Sum +=f2;
f2res->noCpg.counterSites++;
}
if( isSitePotentialTransition ){
f2res->transitions.f2Sum +=f2;
f2res->transitions.counterSites++;
}else{
f2res->transversions.f2Sum +=f2;
f2res->transversions.counterSites++;
}
if( !isSitePotentialDamage ){
f2res->noDamage.f2Sum +=f2;
f2res->noDamage.counterSites++;
}//TODO check!
return false;
}