static void
convert_cat(String *cap, char *s, Config *c, int maxlen)
{
int res;
if (config_get_boolean(c, "/enfle/plugins/ui/normal/filename_code_conversion", &res)) {
char **froms = config_get_list(c, "/enfle/plugins/ui/normal/filename_code_from", &res);
char *to = config_get_str(c, "/enfle/plugins/ui/normal/filename_code_to");
char *from;
int i = 0;
if (res && to) {
while ((from = froms[i++])) {
char *tmp;
//debug_message_fnc("%s->%s: %s\n", from, to, s);
if ((res = converter_convert(s, &tmp, strlen(s), from, to)) < 0)
continue;
if (maxlen)
string_ncat(cap, tmp, maxlen);
else
string_cat(cap, tmp);
free(tmp);
return;
}
}
}
if (maxlen > 0)
string_ncat(cap, s, maxlen);
else
string_cat(cap, s);
}
void plugins_load_all()
{
GSList *plugins_to_load;
plugins_to_load = config_get_list("plugins", NULL);;
g_slist_foreach(plugins_to_load,
(GFunc) tetris_plugin_file_load, NULL);
g_slist_free_full(plugins_to_load, (GDestroyNotify) g_free);
}
/*
Called once at startup, allows to initialize local variables.
Return 1 to suppress VCF/BCF header from printing, 0 for standard
VCF/BCF output and -1 on critical errors.
*/
int init(const char *opts, bcf_hdr_t *in, bcf_hdr_t *out)
{
int i, id;
in_hdr = in;
tags = config_get_list(opts ? opts : "tags=PL,GL,GT","tags", &ntags);
for (i=0; i<ntags; i++)
{
if ( !strcmp("PL",tags[i]) )
{
id = bcf_hdr_id2int(in_hdr,BCF_DT_ID,"PL");
if ( bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,id) )
{
pl_type = bcf_hdr_id2type(in_hdr,BCF_HL_FMT,id);
if ( pl_type!=BCF_HT_INT && pl_type!=BCF_HT_REAL )
{
fprintf(stderr,"Expected numeric type of FORMAT/PL\n");
return -1;
}
handlers = (dosage_f*) realloc(handlers,(nhandlers+1)*sizeof(*handlers));
handlers[nhandlers++] = calc_dosage_PL;
}
}
else if ( !strcmp("GL",tags[i]) )
{
id = bcf_hdr_id2int(in_hdr,BCF_DT_ID,"GL");
if ( bcf_hdr_idinfo_exists(in_hdr,BCF_HL_FMT,id) )
{
gl_type = bcf_hdr_id2type(in_hdr,BCF_HL_FMT,id);
if ( gl_type!=BCF_HT_INT && gl_type!=BCF_HT_REAL )
{
fprintf(stderr,"Expected numeric type of FORMAT/GL\n");
return -1;
}
handlers = (dosage_f*) realloc(handlers,(nhandlers+1)*sizeof(*handlers));
handlers[nhandlers++] = calc_dosage_GL;
}
}
else if ( !strcmp("GT",tags[i]) )
{
handlers = (dosage_f*) realloc(handlers,(nhandlers+1)*sizeof(*handlers));
handlers[nhandlers++] = calc_dosage_GT;
}
else
{
fprintf(stderr,"No handler for tag \"%s\"\n", tags[i]);
return -1;
}
}
free(tags[0]);
free(tags);
printf("#[1]CHROM\t[2]POS\t[3]REF\t[4]ALT");
for (i=0; i<bcf_hdr_nsamples(in_hdr); i++) printf("\t[%d]%s", i+5,in_hdr->samples[i]);
printf("\n");
return 1;
}
