#define VC_CALL_GT 2048
#define VC_ADJLD 4096
#define VC_NO_INDEL 8192
+#define VC_FOLDED 16384
typedef struct {
int flag, prior_type, n1;
if ((p = strstr(b->info, "I16=")) == 0) return -1;
p += 4;
for (i = 0; i < 16; ++i) {
- anno[i] = strtol(p, &p, 10);
+ errno = 0; anno[i] = strtol(p, &p, 10);
if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
++p;
}
tid = begin = end = -1;
memset(&vc, 0, sizeof(viewconf_t));
vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.;
- while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:I")) >= 0) {
+ while ((c = getopt(argc, argv, "fN1:l:cHAGvbSuP:t:p:QgLi:I")) >= 0) {
switch (c) {
+ case 'f': vc.flag |= VC_FOLDED; break;
case '1': vc.n1 = atoi(optarg); break;
case 'l': vc.fn_list = strdup(optarg); break;
case 'N': vc.flag |= VC_ACGT_ONLY; break;
fprintf(stderr, " -Q output the QCALL likelihood format\n");
fprintf(stderr, " -L calculate LD for adjacent sites\n");
fprintf(stderr, " -I skip indels\n");
+ fprintf(stderr, " -f reference-free variant calling\n");
fprintf(stderr, " -1 INT number of group-1 samples [0]\n");
fprintf(stderr, " -l FILE list of sites to output [all sites]\n");
fprintf(stderr, " -t FLOAT scaled substitution mutation rate [%.4lg]\n", vc.theta);
bcf_p1_set_n1(p1, vc.n1);
bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
}
- if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac);
+ if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
+ if (vc.flag & VC_FOLDED) bcf_p1_set_folded(p1);
}
if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {