}
if (conf->vcf) {
double f0, f, fpost, pref = -1.0; // the reference allele frequency
- int j, _ref, _alt, _ref0, depth, rms_q, _ref0b, is_var = 0, qref = 0;
+ int j, _ref, _alt, _ref0, depth, rms_q, _ref0b, is_var = 0, qref = 0, filtered = 0;
uint64_t sqr_sum;
_ref0 = _ref0b = (ref && pos < ref_len)? ref[pos] : 'N';
_ref0 = bam_nt16_nt4_table[bam_nt16_table[_ref0]];
qref = (int)(-3.434 * log(q) + .499);
if (qref > 99) qref = 99;
}
+ filtered = (f >= 0. && f <= 1.)? 0 : 1;
if (conf->var_only && !is_var) continue;
printf("%s\t%d\t.\t%c\t", h->target_name[tid], pos + 1, _ref0b);
if (is_var) {
else printf("%c,%c", "ACGTN"[_ref], "ACGTN"[_alt]);
} else putchar('.');
printf("\t%d\t", qref);
- if (f0 < 0.) printf("Q13\t");
+ if (filtered) printf("Q13\t");
else printf(".\t");
for (i = depth = 0, sqr_sum = 0; i < n; ++i) {
depth += n_plp[i];