-
Notifications
You must be signed in to change notification settings - Fork 1
/
novoCaller.cpp
79 lines (64 loc) · 1.73 KB
/
novoCaller.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
#include <iostream>
#include <vector>
#include <list>
#include <map>
#include <sstream>
#include <string>
#include <fstream>
#include <stdexcept>
#include <cstdlib>
#include <ctime>
#include <cmath>
#include <limits>
#include <algorithm>
#include <sstream>
#include "definitions.h"
#include "tests.h"
int main(int argc,char** argv){
std::string arg1,arg2,arg3,arg4,arg5,arg6,arg7;
for(int i(0);i<argc;++i){
if(std::string(argv[i])=="-a1")
arg1=argv[i+1];
if(std::string(argv[i])=="-a2")
arg2=argv[i+1];
if(std::string(argv[i])=="-a3")
arg3=argv[i+1];
if(std::string(argv[i])=="-a4")
arg4=argv[i+1];
if(std::string(argv[i])=="-a5")
arg5=argv[i+1];
if(std::string(argv[i])=="-a6")
arg6=argv[i+1];
if(std::string(argv[i])=="-a7")
arg7=argv[i+1];
}
{
using namespace std;
string infilename,trio_ID_filename,outfilename,fasta_filename,X_choice;
double PP_thresh,ExAC_thresh;
for(int i(0);i<argc;++i){
if(std::string(argv[i])=="-I")
infilename=argv[i+1];
if(std::string(argv[i])=="-T")
trio_ID_filename=argv[i+1];
if(std::string(argv[i])=="-O")
outfilename=argv[i+1];
if(std::string(argv[i])=="-X")
X_choice=argv[i+1];
if(std::string(argv[i])=="-P")
PP_thresh=atof( argv[i+1] );
if(std::string(argv[i])=="-E")
ExAC_thresh=atof( argv[i+1] );
}
cout<<"infilename="<<infilename<<"\n";
cout<<"trio_ID_filename="<<trio_ID_filename<<"\n";
cout<<"outfilename="<<outfilename<<"\n";
cout<<"X_choice="<<X_choice<<"\n";
cout<<"PP_thresh="<<PP_thresh<<"\n";
cout<<"ExAC_thresh="<<ExAC_thresh<<"\n";
ifstream fin(infilename.c_str());
ofstream fout(outfilename.c_str());
denovo_worker(fin,trio_ID_filename,fout,X_choice,PP_thresh,ExAC_thresh);
}
return 0;
}