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
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
|
/* The MIT License
Copyright (c) 2014 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 "annotate_regions.h"
namespace
{
class Igor : Program
{
public:
std::string version;
///////////
//options//
///////////
std::string input_vcf_file;
std::string ref_fasta_file;
std::string output_vcf_file;
std::vector<GenomeInterval> intervals;
std::string interval_list;
std::string regions_file;
std::string REGIONS_TAG;
std::string REGIONS_TAG_DESC;
std::string REGIONS_LEFT_TAG;
std::string REGIONS_LEFT_TAG_DESC;
std::string REGIONS_RIGHT_TAG;
std::string REGIONS_RIGHT_TAG_DESC;
uint32_t left_window;
uint32_t right_window;
bool without_regions;
bool use_bed;
///////
//i/o//
///////
BCFOrderedReader *odr;
BCFOrderedWriter *odw;
//////////
//filter//
//////////
std::vector<std::string> fexps;
Filter filter;
bool filter_exists;
/////////
//stats//
/////////
int32_t no_variants_annotated;
int32_t no_variants;
////////////////
//common tools//
////////////////
VariantManip *vm;
OrderedRegionOverlapMatcher *orom_regions;
OrderedBCFOverlapMatcher *obom_regions;
Igor(int argc, char **argv)
{
version = "0.5";
//////////////////////////
//options initialization//
//////////////////////////
try
{
std::string desc = "annotates regions in a VCF file";
TCLAP::CmdLine cmd(desc, ' ', version);
VTOutput my; cmd.setOutput(&my);
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, "", "str", cmd);
TCLAP::ValueArg<std::string> arg_output_vcf_file("o", "o", "output VCF file [-]", false, "-", "str", cmd);
TCLAP::ValueArg<std::string> arg_regions_file("b", "b", "regions BED/BCF file []", true, "", "str", cmd);
TCLAP::ValueArg<std::string> arg_REGIONS_TAG("t", "t", "regions tag []", true, "", "str", cmd);
TCLAP::ValueArg<std::string> arg_REGIONS_TAG_DESC("d", "d", "regions tag description []", true, "", "str", cmd);
TCLAP::ValueArg<std::string> arg_fexp("f", "f", "filter expression []", false, "", "str", cmd);
TCLAP::ValueArg<uint32_t> arg_left_window("l", "l", "left window size for overlap []", false, 0, "int", cmd);
TCLAP::ValueArg<uint32_t> arg_right_window("r", "r", "right window size for overlap []", false, 0, "int", cmd);
TCLAP::SwitchArg arg_without_regions("w", "w", "outside of (without) regions", cmd, false);
TCLAP::UnlabeledValueArg<std::string> arg_input_vcf_file("<in.vcf>", "input VCF file", true, "","file", cmd);
cmd.parse(argc, argv);
input_vcf_file = arg_input_vcf_file.getValue();
output_vcf_file = arg_output_vcf_file.getValue();
parse_intervals(intervals, arg_interval_list.getValue(), arg_intervals.getValue());
parse_filters(fexps, arg_fexp.getValue(), 2, false);
regions_file = arg_regions_file.getValue();
left_window = arg_left_window.getValue();
right_window = arg_right_window.getValue();
without_regions = arg_without_regions.getValue();
REGIONS_TAG = arg_REGIONS_TAG.getValue();
REGIONS_TAG_DESC = arg_REGIONS_TAG_DESC.getValue();
REGIONS_LEFT_TAG = REGIONS_TAG + "_LEFT";
REGIONS_RIGHT_TAG = REGIONS_TAG + "_RIGHT";
}
catch (TCLAP::ArgException &e)
{
std::cerr << "error: " << e.error() << " for arg " << e.argId() << std::endl;
abort();
}
};
~Igor() {};
void initialize()
{
////////////////////
//i/o initialization
////////////////////
odr = new BCFOrderedReader(input_vcf_file, intervals);
odw = new BCFOrderedWriter(output_vcf_file);
odw->link_hdr(odr->hdr);
std::string hrec = "##INFO=<ID=" + REGIONS_TAG + ",Number=0,Type=Flag,Description=\"" + REGIONS_TAG_DESC + "\">";
bcf_hdr_append(odw->hdr, hrec.c_str());
if (left_window)
{
std::string hrec = "##INFO=<ID=" + REGIONS_LEFT_TAG + ",Number=0,Type=Flag,Description=\"" + REGIONS_TAG_DESC + " (Left window)\">";
bcf_hdr_append(odw->hdr, hrec.c_str());
}
if (right_window)
{
std::string hrec = "##INFO=<ID=" + REGIONS_RIGHT_TAG + ",Number=0,Type=Flag,Description=\"" + REGIONS_TAG_DESC + " (Right window)\">";
bcf_hdr_append(odw->hdr, hrec.c_str());
}
/////////////////////////
//filter initialization//
/////////////////////////
filter.parse(fexps[0].c_str(), false);
filter_exists = fexps[0]=="" ? false : true;
///////////////////////
//tool initialization//
///////////////////////
if (str_ends_with(regions_file, ".bed") || str_ends_with(regions_file, ".bed.gz"))
{
use_bed = true;
orom_regions = new OrderedRegionOverlapMatcher(regions_file);
}
else if (str_ends_with(regions_file, ".vcf") || str_ends_with(regions_file, ".vcf.gz") || str_ends_with(regions_file, ".bcf"))
{
use_bed = false;
obom_regions = new OrderedBCFOverlapMatcher(regions_file, intervals, fexps[1]);
}
else
{
fprintf(stderr, "[%s:%d %s] Need to at least specify either a bed or bcf file\n", __FILE__, __LINE__, __FUNCTION__);
exit(1);
}
////////////////////////
//stats initialization//
////////////////////////
no_variants_annotated = 0;
no_variants = 0;
}
void print_options()
{
std::clog << "annotate_regions v" << version << "\n";
std::clog << "\n";
std::clog << "options: input VCF file(s) " << input_vcf_file << "\n";
std::clog << " [o] output VCF file " << output_vcf_file << "\n";
print_str_op(" [f] filter 1 ", fexps[0]);
print_str_op(" filter 2 ", fexps[1]);
print_str_op(" [t] region INFO tag ", REGIONS_TAG);
print_str_op(" [d] region INFO description ", REGIONS_TAG_DESC);
print_str_op(" [b] regions file ", regions_file);
print_boo_op(" [w] without regions ", without_regions);
print_num_op(" [l] left window ", left_window);
print_num_op(" [r] right window ", right_window);
print_int_op(" [i] intervals ", intervals);
std::clog << "\n";
}
void print_stats()
{
std::clog << "\n";
std::cerr << "stats: no. of variants annotated " << no_variants_annotated << "\n";
std::cerr << " total no. of variants " << no_variants << "\n";std::clog << "\n";
}
void annotate_regions()
{
odw->write_hdr();
bcf_hdr_t *h = odr->hdr;
bcf1_t *v = bcf_init1();
std::vector<Interval*> overlaps;
Variant variant;
kstring_t s = {0,0,0};
while (odr->read(v))
{
bcf_unpack(v, BCF_UN_STR);
if (filter_exists)
{
vm->classify_variant(h, v, variant);
if (!filter.apply(h, v, &variant, false))
{
continue;
}
}
std::string chrom = bcf_get_chrom(odr->hdr,v);
int32_t beg1 = bcf_get_pos1(v);
int32_t end1 = bcf_get_end1(v);
if (use_bed)
{
bool overlaps = orom_regions->overlaps_with(chrom, beg1-left_window, end1+right_window);
if (!without_regions && overlaps)
{
if (left_window+right_window)
{
std::vector<Interval>& regs = orom_regions->overlapping_regions;
for (int32_t i=0; i<regs.size(); ++i)
{
if (beg1>=regs[i].beg1-left_window && beg1<=regs[i].beg1+right_window)
{
bcf_update_info_flag(odr->hdr, v, REGIONS_LEFT_TAG.c_str(), "", 1);
}
else if (end1>=regs[i].end1-right_window && end1<=regs[i].end1+right_window)
{
bcf_update_info_flag(odr->hdr, v, REGIONS_RIGHT_TAG.c_str(), "", 1);
}
}
}
bcf_update_info_flag(odr->hdr, v, REGIONS_TAG.c_str(), "", 1);
++no_variants_annotated;
}
else if (without_regions && !overlaps)
{
bcf_update_info_flag(odr->hdr, v, REGIONS_TAG.c_str(), "", 1);
++no_variants_annotated;
}
}
else
{
bool overlaps = orom_regions->overlaps_with(chrom, beg1-left_window, end1+right_window);
if (!without_regions && overlaps)
{
bcf_update_info_flag(odr->hdr, v, REGIONS_TAG.c_str(), "", 1);
++no_variants_annotated;
}
else if (without_regions && !overlaps)
{
bcf_update_info_flag(odr->hdr, v, REGIONS_TAG.c_str(), "", 1);
++no_variants_annotated;
}
}
++no_variants;
odw->write(v);
}
odw->close();
};
private:
};
}
void annotate_regions(int argc, char ** argv)
{
Igor igor(argc, argv);
igor.print_options();
igor.initialize();
igor.annotate_regions();
igor.print_stats();
};
|
