- c->l_qseq = strlen(str->s);
- if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
- parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
- p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
- memset(p, 0, (c->l_qseq+1)/2);
- for (i = 0; i < c->l_qseq; ++i)
- p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
+ if (strcmp(str->s, "*")) {
+ c->l_qseq = strlen(str->s);
+ if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
+ parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
+ p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
+ memset(p, 0, (c->l_qseq+1)/2);
+ for (i = 0; i < c->l_qseq; ++i)
+ p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
+ } else c->l_qseq = 0;