61     int32_t oplen;  in initialize()  local
79         oplen = bam_cigar_oplen(cigar[i]);  in initialize()
93             rpos0 += oplen;  in initialize()
98             uint32_t mlen = oplen; //match length  in initialize()
236                 aug_cigar.push_back(bam_cigar_gen(oplen, BAM_CSOFT_CLIP));  in initialize()
240                 rpos0 += oplen;  in initialize()
245                 aug_cigar.push_back(bam_cigar_gen(oplen, BAM_CSOFT_CLIP));  in initialize()
249                 rpos0 += oplen;  in initialize()
256                 for (size_t i=0; i<oplen ; ++i)  in initialize()
261                 aug_cigar.push_back(bam_cigar_gen(oplen, BAM_CINS));  in initialize()
265                 rpos0 += oplen;  in initialize()
281         uint32_t oplen = bam_cigar_oplen(aug_cigar[i]);  in initialize()  local
286             rpos0 += oplen;  in initialize()
290             rpos0 += oplen;  in initialize()
291             end1 +=oplen;  in initialize()
304             rpos0 += oplen;  in initialize()
310             end1 +=oplen;  in initialize()
389             int32_t oplen = bam_cigar_oplen(aug_cigar[i]);  in print()  local
432             int32_t oplen = bam_cigar_oplen(aug_cigar[i]);  in print()  local
447     int32_t oplen;  in print()  local
453         oplen = bam_cigar_oplen(aug_cigar[i]);  in print()
456         std::cerr << oplen << opchr;  in print()
470         oplen = bam_cigar_oplen(aug_cigar[i]);  in print()
475             ref.append(oplen, '-');  in print()
477             for (uint32_t j=0; j<oplen; ++j)  in print()
483             align.append(oplen, 'S');  in print()
487             for (uint32_t j=0; j<oplen; ++j)  in print()
493             align.append(oplen, '=');  in print()
495             spos0 += oplen;  in print()
510             ref.append(oplen, '-');  in print()
512             align.append( oplen, 'I');  in print()
514             for (uint32_t j=0; j<oplen; ++j)  in print()
519             spos0 += oplen;  in print()
524             seq.append(oplen, '-');  in print()
525             align.append(oplen, 'D');  in print()