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
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
|
/*
vcflib C++ library for parsing and manipulating VCF files
Copyright © 2010-2020 Erik Garrison
Copyright © 2020 Pjotr Prins
This software is published under the MIT License. See the LICENSE file.
*/
#include "Variant.h"
#include "split.h"
#include <getopt.h>
using namespace std;
using namespace vcflib;
void printSummary(char** argv) {
cerr << "usage: " << argv[0] << " [options] <vcf file>" << endl
<< endl
<< "Adjust GLs so that the maximum GL is 0 by dividing all GLs for each sample by the max." << endl << endl
<< "Then cap (bound) at N (e.g. -10)."
<< "options:" << endl
<< " -b, --bound N Bound GLs to this limit." << endl
<< " -x, --exclude-broken If GLs are > 0, remove site." << endl
<< endl;
cerr << endl << "Type: transformation" << endl << endl;
exit(0);
}
int main(int argc, char** argv) {
bool excludeBroken = false;
double glBound = 0;
int c;
while (true) {
static struct option long_options[] =
{
/* These options set a flag. */
//{"verbose", no_argument, &verbose_flag, 1},
{"help", no_argument, 0, 'h'},
{"bound", required_argument, 0, 'b'},
{"exclude-broken", no_argument, 0, 'x'},
//{"length", no_argument, &printLength, true},
{0, 0, 0, 0}
};
/* getopt_long stores the option index here. */
int option_index = 0;
c = getopt_long (argc, argv, "hxb:",
long_options, &option_index);
/* Detect the end of the options. */
if (c == -1)
break;
switch (c)
{
case 0:
/* If this option set a flag, do nothing else now. */
if (long_options[option_index].flag != 0)
break;
printf ("option %s", long_options[option_index].name);
if (optarg)
printf (" with arg %s", optarg);
printf ("\n");
break;
case 'b':
glBound = atof(optarg);
break;
case 'x':
excludeBroken = true;
break;
case 'h':
printSummary(argv);
exit(0);
break;
case '?':
/* getopt_long already printed an error message. */
printSummary(argv);
exit(1);
break;
default:
abort ();
}
}
if (glBound == 0) {
cerr << "a bound is required when running vcfglbound (try -10)" << endl;
exit(1);
}
VariantCallFile variantFile;
string inputFilename;
if (optind == argc - 1) {
inputFilename = argv[optind];
variantFile.open(inputFilename);
} else {
variantFile.open(std::cin);
}
if (!variantFile.is_open()) {
return 1;
}
cout << variantFile.header << endl;
Variant var(variantFile);
while (variantFile.getNextVariant(var)) {
if (find(var.format.begin(), var.format.end(), "GL") == var.format.end()) {
cout << var << endl;
continue;
}
if (find(var.format.begin(), var.format.end(), "GT") == var.format.end()) {
var.format.push_back("GT");
reverse(var.format.begin(), var.format.end());
}
bool isbroken = false;
for (map<string, map<string, vector<string> > >::iterator s = var.samples.begin();
s != var.samples.end(); ++s) {
map<string, vector<string> >& sample = s->second;
map<string, vector<string> >::iterator l = sample.find("GL");
if (l != sample.end()) {
// find the gl max
vector<string>& glstrs = l->second;
vector<double> gls;
for (vector<string>::iterator gl = glstrs.begin(); gl != glstrs.end(); ++gl) {
double d;
convert(*gl, d);
gls.push_back(d);
}
isbroken = false; // reset every iteration
for (vector<double>::iterator g = gls.begin(); g != gls.end(); ++g) {
if (*g > 0) {
isbroken = true;
break;
}
}
if (isbroken) {
if (excludeBroken) {
cerr << var.sequenceName << ":" << var.position << ", sample " << s->first << " has GL > 0" << endl;
break;
} else {
cerr << "VCF record @ " << var.sequenceName << ":" << var.position << ", sample " << s->first << " has GL > 0, not processing, but outputting" << endl;
continue;
}
}
// normalize GLs to -10 min 0 max using division by max and bounding at -10
double minGL = 0;
for (vector<double>::iterator g = gls.begin(); g != gls.end(); ++g) {
if (*g < minGL) minGL = *g;
}
double maxGL = minGL;
for (vector<double>::iterator g = gls.begin(); g != gls.end(); ++g) {
if (*g > maxGL) maxGL = *g;
}
// modify gls
for (vector<double>::iterator g = gls.begin(); g != gls.end(); ++g) {
*g = max(glBound, *g - maxGL);
}
// and pack back into GL field
glstrs.clear();
for (vector<double>::iterator g = gls.begin(); g != gls.end(); ++g) {
glstrs.push_back(convert(*g));
}
}
}
if (excludeBroken && isbroken) {
cerr << "excluding VCF record @ " << var.sequenceName << ":" << var.position << " due to GLs > 0" << endl;
} else {
cout << var << endl;
}
}
return 0;
}
|
