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
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
|
/* The MIT License
Copyright (c) 2016 Adrian Tan <atks@umich.edu>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
*/
#include "svm_predict.h"
namespace
{
class Igor : Program
{
public:
std::string version;
///////////
//options//
///////////
std::string input_vcf_file;
std::vector<std::string> input_vcf_files;
std::string ref_fasta_file;
std::string ref_data_sets_list;
std::vector<GenomeInterval> intervals;
std::string interval_list;
///////
//i/o//
///////
BCFOrderedReader *odr;
bcf1_t *v;
kstring_t line;
//////////
//filter//
//////////
std::string fexp;
Filter filter;
bool filter_exists;
/////////
//stats//
/////////
int32_t no_snps;
////////////////
//common tools//
////////////////
VariantManip *vm;
Igor(int argc, char ** argv)
{
//////////////////////////
//options initialization//
//////////////////////////
try
{
std::string desc = "svm_predict";
version = "0.5";
TCLAP::CmdLine cmd(desc, ' ', version);
VTOutput my; cmd.setOutput(&my);
TCLAP::ValueArg<std::string> arg_model_file("r", "r", "reference sequence fasta file []", true, "", "str", cmd);
TCLAP::ValueArg<std::string> arg_intervals("i", "i", "intervals []", false, "", "str", cmd);
TCLAP::ValueArg<std::string> arg_interval_list("I", "I", "file containing list of intervals []", false, "", "file", cmd);
TCLAP::ValueArg<std::string> arg_fexp("f", "f", "filter expression []", false, "VTYPE==SNP", "str", cmd);
TCLAP::UnlabeledValueArg<std::string> arg_input_vcf_file("<in.vcf>", "input VCF file", true, "","file", cmd);
cmd.parse(argc, argv);
parse_intervals(intervals, arg_interval_list.getValue(), arg_intervals.getValue());
fexp = arg_fexp.getValue();
input_vcf_file = arg_input_vcf_file.getValue();
}
catch (TCLAP::ArgException &e)
{
std::cerr << "error: " << e.error() << " for arg " << e.argId() << "\n";
abort();
}
};
void initialize()
{
/////////////////////////
//filter initialization//
/////////////////////////
filter.parse(fexp.c_str(), false);
filter_exists = fexp=="" ? false : true;
//////////////////////
//i/o initialization//
//////////////////////
odr = new BCFOrderedReader(input_vcf_file, intervals);
///////////////////////
//tool initialization//
///////////////////////
vm = new VariantManip(ref_fasta_file);
////////////////////////
//stats initialization//
////////////////////////
}
void svm_predict()
{
Variant variant;
bcf1_t *v = bcf_init1();
while(odr->read(v))
{
//apply model
//add SVM score
//write out
}
};
void print_options()
{
std::clog << "svm_predict v" << version << "\n\n";
std::clog << "\n";
std::clog << "Options: input VCF File " << input_vcf_file << "\n";
print_str_op(" [f] filter ", fexp);
print_int_op(" [i] intervals ", intervals);
std::clog << "\n\n";
}
void print_stats()
{
};
~Igor()
{
};
private:
};
}
void svm_predict(int argc, char ** argv)
{
Igor igor(argc, argv);
igor.print_options();
igor.initialize();
igor.svm_predict();
igor.print_stats();
}
|
