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/*
Copyright (C) 2016 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 <getopt.h>
#include <stdarg.h>
#include <stdint.h>
#include <htslib/vcf.h>
#include <htslib/synced_bcf_reader.h>
#include <htslib/vcfutils.h>
#include <inttypes.h>
#include <unistd.h>
#include <errno.h>
#include "bcftools.h"
#include "smpl_ilist.h"
typedef struct
{
int argc, output_type, regions_is_file, targets_is_file;
char **argv, *output_fname, *regions_list, *targets_list;
int32_t *arr_a, narr_a, *arr_b, narr_b;
bcf_srs_t *sr;
bcf_hdr_t *hdr_a, *hdr_b;
htsFile *out_fh;
}
args_t;
const char *about(void)
{
return "Compare two files and set non-identical genotypes to missing.\n";
}
static const char *usage_text(void)
{
return
"\n"
"About: Compare two files and set non-identical genotypes in the first file to missing.\n"
"\n"
"Usage: bcftools +isecGT <A.bcf> <B.bcf> [Plugin Options]\n"
"Plugin options:\n"
" -o, --output <file> write output to a 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";
}
int run(int argc, char **argv)
{
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->output_fname = "-";
args->output_type = FT_VCF;
static struct option loptions[] =
{
{"regions",required_argument,NULL,'r'},
{"regions-file",required_argument,NULL,'R'},
{"targets",required_argument,NULL,'t'},
{"targets-file",required_argument,NULL,'T'},
{"output",required_argument,NULL,'o'},
{"output-type",required_argument,NULL,'O'},
{NULL,0,NULL,0}
};
int c;
while ((c = getopt_long(argc, argv, "o:O:r:R:t:T:",loptions,NULL)) >= 0)
{
switch (c)
{
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 'r': args->regions_list = optarg; break;
case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
case 't': args->targets_list = optarg; break;
case 'T': args->targets_list = optarg; args->targets_is_file = 1; break;
case 'h':
case '?':
default: error("%s", usage_text()); break;
}
}
if ( optind+2!=argc ) error("%s",usage_text());
args->sr = bcf_sr_init();
args->sr->require_index = 1;
if ( args->regions_list )
{
if ( bcf_sr_set_regions(args->sr, args->regions_list, args->regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
}
if ( args->targets_list )
{
if ( bcf_sr_set_targets(args->sr, args->targets_list, args->targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
args->sr->collapse |= COLLAPSE_BOTH;
}
if ( !bcf_sr_add_reader(args->sr,argv[optind]) ) error("Error opening %s: %s\n", argv[optind],bcf_sr_strerror(args->sr->errnum));
if ( !bcf_sr_add_reader(args->sr,argv[optind+1]) ) error("Error opening %s: %s\n", argv[optind+1],bcf_sr_strerror(args->sr->errnum));
args->hdr_a = bcf_sr_get_header(args->sr,0);
args->hdr_b = bcf_sr_get_header(args->sr,1);
smpl_ilist_t *smpl = smpl_ilist_map(args->hdr_a, args->hdr_b, SMPL_STRICT);
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));
bcf_hdr_write(args->out_fh, args->hdr_a);
while ( bcf_sr_next_line(args->sr) )
{
if ( !bcf_sr_has_line(args->sr,0) ) continue;
if ( !bcf_sr_has_line(args->sr,1) )
{
bcf_write(args->out_fh, args->hdr_a, bcf_sr_get_line(args->sr,0));
continue;
}
bcf1_t *line_a = bcf_sr_get_line(args->sr,0);
bcf1_t *line_b = bcf_sr_get_line(args->sr,1);
int ngt_a = bcf_get_genotypes(args->hdr_a, line_a, &args->arr_a, &args->narr_a);
int ngt_b = bcf_get_genotypes(args->hdr_b, line_b, &args->arr_b, &args->narr_b);
assert( ngt_a==ngt_b ); // todo
ngt_a /= smpl->n;
ngt_b /= smpl->n;
int i, j, dirty = 0;
for (i=0; i<smpl->n; i++)
{
int32_t *a = args->arr_a + i*ngt_a;
int32_t *b = args->arr_b + smpl->idx[i]*ngt_b;
for (j=0; j<ngt_a; j++)
if ( a[j]!=b[j] ) break;
if ( j<ngt_a )
{
dirty = 1;
for (j=0; j<ngt_a; j++) a[j] = bcf_gt_missing;
}
}
if ( dirty ) bcf_update_genotypes(args->hdr_a, line_a, args->arr_a, ngt_a*smpl->n);
bcf_write(args->out_fh, args->hdr_a, line_a);
}
if ( hts_close(args->out_fh)!=0 ) error("Close failed: %s\n",args->output_fname);
smpl_ilist_destroy(smpl);
bcf_sr_destroy(args->sr);
free(args->arr_a);
free(args->arr_b);
free(args);
return 0;
}
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