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
|
/*
Copyright (C) 2017-2019 Genome Research Ltd.
Author: Petr Danecek <pd3@sanger.ac.uk>
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 <stdio.h>
#include <stdlib.h>
#include <strings.h>
#include <getopt.h>
#include <stdarg.h>
#include <unistd.h>
#include <stdint.h>
#include <errno.h>
#include <inttypes.h>
#include <htslib/vcf.h>
#include <htslib/synced_bcf_reader.h>
#include <htslib/vcfutils.h>
#include "bcftools.h"
#include "vcfbuf.h"
#include "filter.h"
#define FLT_INCLUDE 1
#define FLT_EXCLUDE 2
typedef struct
{
filter_t *filter;
char *filter_str;
int filter_logic; // one of FLT_INCLUDE/FLT_EXCLUDE (-i or -e)
vcfbuf_t *vcfbuf;
int argc, region_is_file, target_is_file, output_type, verbose, nrm, ntot, print_overlaps, rmdup;
char **argv, *region, *target, *fname, *output_fname;
htsFile *out_fh;
bcf_hdr_t *hdr;
bcf_srs_t *sr;
}
args_t;
const char *about(void)
{
return "Remove overlapping variants\n";
}
static const char *usage_text(void)
{
return
"\n"
"About: Remove overlapping variants.\n"
"\n"
"Usage: bcftools +remove-overlaps [Options]\n"
"Plugin options:\n"
" -d, --rm-dup remove only duplicate sites and remove them completely\n"
" -p, --print-overlaps do the opposite and print only overlapping sites\n"
" -v, --verbose print a list of removed sites\n"
"Standard options:\n"
" -e, --exclude EXPR exclude sites for which the expression is true\n"
" -i, --include EXPR include only sites for which the expression is true\n"
" -o, --output FILE write output to the FILE [standard output]\n"
" -O, --output-type b|u|z|v b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n"
" -r, --regions REGION restrict to comma-separated list of regions\n"
" -R, --regions-file FILE restrict to regions listed in a file\n"
" -t, --targets REGION similar to -r but streams rather than index-jumps\n"
" -T, --targets-file FILE similar to -R but streams rather than index-jumps\n"
"\n";
}
static void init_data(args_t *args)
{
args->sr = bcf_sr_init();
if ( args->region )
{
args->sr->require_index = 1;
if ( bcf_sr_set_regions(args->sr, args->region, args->region_is_file)<0 ) error("Failed to read the regions: %s\n",args->region);
}
if ( args->target && bcf_sr_set_targets(args->sr, args->target, args->target_is_file, 0)<0 ) error("Failed to read the targets: %s\n",args->target);
if ( !bcf_sr_add_reader(args->sr,args->fname) ) error("Error: %s\n", bcf_sr_strerror(args->sr->errnum));
args->hdr = bcf_sr_get_header(args->sr,0);
args->out_fh = hts_open(args->output_fname,hts_bcf_wmode(args->output_type));
if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
if ( bcf_hdr_write(args->out_fh, args->hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
args->vcfbuf = vcfbuf_init(args->hdr, 0);
if ( args->rmdup )
vcfbuf_set_opt(args->vcfbuf,int,VCFBUF_RMDUP,1)
else
vcfbuf_set_opt(args->vcfbuf,int,VCFBUF_OVERLAP_WIN,1)
if ( args->filter_str )
args->filter = filter_init(args->hdr, args->filter_str);
}
static void destroy_data(args_t *args)
{
if ( args->filter )
filter_destroy(args->filter);
if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
vcfbuf_destroy(args->vcfbuf);
bcf_sr_destroy(args->sr);
free(args);
}
static void flush(args_t *args, int flush_all)
{
int nbuf = vcfbuf_nsites(args->vcfbuf);
bcf1_t *rec;
while ( (rec = vcfbuf_flush(args->vcfbuf, flush_all)) )
{
if ( nbuf>2 || (nbuf>1 && flush_all) )
{
args->nrm++;
if ( args->verbose ) printf("%s\t%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
if ( args->print_overlaps && bcf_write1(args->out_fh, args->hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
continue; // skip overlapping variants
}
if ( !args->print_overlaps && bcf_write1(args->out_fh, args->hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
}
}
static void process(args_t *args)
{
args->ntot++;
bcf1_t *rec = bcf_sr_get_line(args->sr,0);
if ( args->filter )
{
int ret = filter_test(args->filter, rec, NULL);
if ( args->filter_logic==FLT_INCLUDE ) { if ( !ret ) return; }
else if ( ret ) return;
}
bcf_sr_t *sr = bcf_sr_get_reader(args->sr, 0);
sr->buffer[0] = vcfbuf_push(args->vcfbuf, rec, 1);
flush(args,0);
}
int run(int argc, char **argv)
{
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->argc = argc; args->argv = argv;
args->output_type = FT_VCF;
args->output_fname = "-";
static struct option loptions[] =
{
{"rm-dup",no_argument,NULL,'d'},
{"print-overlaps",no_argument,NULL,'p'},
{"exclude",required_argument,NULL,'e'},
{"include",required_argument,NULL,'i'},
{"regions",required_argument,NULL,'r'},
{"regions-file",required_argument,NULL,'R'},
{"output",required_argument,NULL,'o'},
{"output-type",required_argument,NULL,'O'},
{"verbose",no_argument,NULL,'v'},
{NULL,0,NULL,0}
};
int c;
while ((c = getopt_long(argc, argv, "r:R:t:T:o:O:i:e:vpd",loptions,NULL)) >= 0)
{
switch (c)
{
case 'd': args->rmdup = 1; break;
case 'p': args->print_overlaps = 1; break;
case 'v': args->verbose = 1; break;
case 'e': args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
case 'i': args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
case 'T': args->target_is_file = 1; // fall-through
case 't': args->target = optarg; break;
case 'R': args->region_is_file = 1; // fall-through
case 'r': args->region = optarg; break;
case 'o': args->output_fname = optarg; break;
case 'O':
switch (optarg[0]) {
case 'b': args->output_type = FT_BCF_GZ; break;
case 'u': args->output_type = FT_BCF; break;
case 'z': args->output_type = FT_VCF_GZ; break;
case 'v': args->output_type = FT_VCF; break;
default: error("The output type \"%s\" not recognised\n", optarg);
}
break;
case 'h':
case '?':
default: error("%s", usage_text()); break;
}
}
if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n");
if ( optind==argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-"; // reading from stdin
else { error("%s",usage_text()); }
}
else if ( optind+1!=argc ) error("%s",usage_text());
else args->fname = argv[optind];
init_data(args);
while ( bcf_sr_next_line(args->sr) ) process(args);
flush(args,1);
fprintf(stderr,"Processed/Removed\t%d\t%d\n",args->ntot,args->nrm);
destroy_data(args);
return 0;
}
|
