int bcf_sr_set_targets(bcf_srs_t *readers, const char *targets, int is_file, int alleles)
{
assert( !readers->targets );
readers->targets = bcf_sr_regions_init(targets,is_file,0,1,-2);
if ( !readers->targets ) return -1;
readers->targets_als = alleles;
return 0;
}
int bcf_sr_set_regions(bcf_srs_t *readers, const char *regions, int is_file)
{
assert( !readers->regions );
if ( readers->nreaders )
{
fprintf(stderr,"[%s:%d %s] Error: bcf_sr_set_regions() must be called before bcf_sr_add_reader()\n", __FILE__,__LINE__,__FUNCTION__);
return -1;
}
readers->regions = bcf_sr_regions_init(regions,is_file,0,1,-2);
if ( !readers->regions ) return -1;
readers->explicit_regs = 1;
readers->require_index = 1;
return 0;
}
int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
{
int c;
char *fname = NULL;
static struct option loptions[] =
{
{"exons",1,0,'e'},
{0,0,0,0}
};
while ((c = getopt_long(argc, argv, "e:?h",loptions,NULL)) >= 0)
{
switch (c)
{
case 'e': fname = optarg; break;
case 'h':
case '?':
default: fprintf(stderr,"%s", usage()); exit(1); break;
}
}
if ( !fname )
{
fprintf(stderr,"Missing the -e option.\n");
return -1;
}
in_hdr = in;
out_hdr = out;
int ret = bcf_hdr_append(out_hdr,"##INFO=<ID=OOF,Number=A,Type=Integer,Description=\"Frameshift Indels: out-of-frame (1), in-frame (0), not-applicable (-1 or missing)\">");
if ( ret!=0 )
{
fprintf(stderr,"Error updating the header\n");
return -1;
}
exons = bcf_sr_regions_init(fname,1,0,1,2);
if ( !exons )
{
fprintf(stderr,"Error occurred while reading (was the file compressed with bgzip?): %s\n", fname);
return -1;
}
return 0;
}
int init(const char *opts, bcf_hdr_t *in, bcf_hdr_t *out)
{
in_hdr = in;
out_hdr = out;
int ret = bcf_hdr_append(out_hdr,"##INFO=<ID=OOF,Number=A,Type=Integer,Description=\"Frameshift Indels: out-of-frame (1), in-frame (0), not-applicable (-1 or missing)\">");
if ( ret!=0 )
{
fprintf(stderr,"Error updating the header\n");
return -1;
}
char *fname = config_get_string(opts,"exons");
if ( !fname )
{
fprintf(stderr,"No exons given, please run as \"bcftools annotate -p frameshifts:exons=path/to/file.tab.gz\".\n");
return -1;
}
wordexp_t wexp;
wordexp(fname, &wexp, 0);
if ( !wexp.we_wordc )
{
fprintf(stderr,"No such file: %s\n", fname);
return -1;
}
free(fname);
fname = wexp.we_wordv[0];
exons = bcf_sr_regions_init(fname,1,0,1,2);
if ( !exons )
{
fprintf(stderr,"Error occurred while reading (was the file compressed with bgzip?): %s\n", fname);
return -1;
}
wordfree(&wexp);
return 0;
}