int main_vcfgtcheck(int argc, char *argv[])
{
int c;
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->files = bcf_sr_init();
args->argc = argc; args->argv = argv; set_cwd(args);
char *regions = NULL, *targets = NULL;
static struct option loptions[] =
{
{"GTs-only",1,0,'G'},
{"all-sites",0,0,'a'},
{"homs-only",0,0,'H'},
{"help",0,0,'h'},
{"genotypes",1,0,'g'},
{"plot",1,0,'p'},
{"target-sample",1,0,'S'},
{"query-sample",1,0,'s'},
{"regions",1,0,'r'},
{"targets",1,0,'t'},
{0,0,0,0}
};
while ((c = getopt_long(argc, argv, "hg:p:s:S:Hr:at:G:",loptions,NULL)) >= 0) {
switch (c) {
case 'G': args->no_PLs = atoi(optarg); break;
case 'a': args->all_sites = 1; break;
case 'H': args->hom_only = 1; break;
case 'g': args->gt_fname = optarg; break;
case 'p': args->plot = optarg; break;
case 'S': args->target_sample = optarg; break;
case 's': args->query_sample = optarg; break;
case 'r': regions = optarg; break;
case 't': targets = optarg; break;
case 'h':
case '?': usage();
default: error("Unknown argument: %s\n", optarg);
}
}
if ( argc==optind || argc>optind+1 ) usage(); // none or too many files given
if ( !args->gt_fname ) args->cross_check = 1; // no genotype file, run in cross-check mode
else args->files->require_index = 1;
if ( regions && bcf_sr_set_regions(args->files, regions)<0 ) error("Failed to read the regions: %s\n", regions);
if ( targets && bcf_sr_set_targets(args->files, targets,0)<0 ) error("Failed to read the targets: %s\n", targets);
if ( !bcf_sr_add_reader(args->files, argv[optind]) ) error("Failed to open or the file not indexed: %s\n", argv[optind]);
if ( args->gt_fname && !bcf_sr_add_reader(args->files, args->gt_fname) ) error("Failed to open or the file not indexed: %s\n", args->gt_fname);
args->files->collapse = COLLAPSE_SNPS|COLLAPSE_INDELS;
if ( args->plot ) args->plot = init_prefix(args->plot);
init_data(args);
if ( args->cross_check )
cross_check_gts(args);
else
check_gt(args);
destroy_data(args);
bcf_sr_destroy(args->files);
if (args->plot) free(args->plot);
free(args);
return 0;
}
int main_vcfgtcheck(int argc, char *argv[])
{
int c;
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->files = bcf_sr_init();
args->argc = argc; args->argv = argv; set_cwd(args);
char *regions = NULL, *targets = NULL;
int regions_is_file = 0, targets_is_file = 0;
static struct option loptions[] =
{
{"GTs-only",1,0,'G'},
{"all-sites",0,0,'a'},
{"homs-only",0,0,'H'},
{"help",0,0,'h'},
{"genotypes",1,0,'g'},
{"plot",1,0,'p'},
{"target-sample",1,0,'S'},
{"query-sample",1,0,'s'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{0,0,0,0}
};
char *tmp;
while ((c = getopt_long(argc, argv, "hg:p:s:S:Hr:R:at:T:G:",loptions,NULL)) >= 0) {
switch (c) {
case 'G':
args->no_PLs = strtol(optarg,&tmp,10);
if ( *tmp ) error("Could not parse argument: --GTs-only %s\n", optarg);
break;
case 'a': args->all_sites = 1; break;
case 'H': args->hom_only = 1; break;
case 'g': args->gt_fname = optarg; break;
case 'p': args->plot = optarg; break;
case 'S': args->target_sample = optarg; break;
case 's': args->query_sample = optarg; break;
case 'r': regions = optarg; break;
case 'R': regions = optarg; regions_is_file = 1; break;
case 't': targets = optarg; break;
case 'T': targets = optarg; targets_is_file = 1; break;
case 'h':
case '?': usage();
default: error("Unknown argument: %s\n", optarg);
}
}
char *fname = NULL;
if ( optind==argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
else usage(); // no files given
}
else fname = argv[optind];
if ( argc>optind+1 ) usage(); // too many files given
if ( !args->gt_fname ) args->cross_check = 1; // no genotype file, run in cross-check mode
else args->files->require_index = 1;
if ( regions && bcf_sr_set_regions(args->files, regions, regions_is_file)<0 ) error("Failed to read the regions: %s\n", regions);
if ( targets && bcf_sr_set_targets(args->files, targets, targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", targets);
if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
if ( args->gt_fname && !bcf_sr_add_reader(args->files, args->gt_fname) ) error("Failed to open %s: %s\n", args->gt_fname,bcf_sr_strerror(args->files->errnum));
args->files->collapse = COLLAPSE_SNPS|COLLAPSE_INDELS;
if ( args->plot ) args->plot = init_prefix(args->plot);
init_data(args);
if ( args->cross_check )
cross_check_gts(args);
else
check_gt(args);
destroy_data(args);
bcf_sr_destroy(args->files);
if (args->plot) free(args->plot);
free(args);
return 0;
}
