Lines Matching refs:oplen
81 int j, oplen = cigar[i]>>4, op = cigar[i]&0xf; in bam_fillmd1_core() local
83 for (j = 0; j < oplen; ++j) { in bam_fillmd1_core()
98 if (j < oplen) break; in bam_fillmd1_core()
99 rpos += oplen; qpos += oplen; in bam_fillmd1_core()
103 for (j = 0; j < oplen; ++j) { in bam_fillmd1_core()
109 if (j < oplen) break; in bam_fillmd1_core()
111 qpos += oplen; in bam_fillmd1_core()
112 if (op == BAM_CINS) nm += oplen; in bam_fillmd1_core()
114 rpos += oplen; in bam_fillmd1_core()
125 int j, oplen = cigar[i]>>4, op = cigar[i]&0xf; in bam_fillmd1_core() local
127 for (j = 0; j < oplen; ++j) { in bam_fillmd1_core()
138 if (j < oplen) break; in bam_fillmd1_core()
139 rpos += oplen; qpos += oplen; in bam_fillmd1_core()
140 } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) rpos += oplen; in bam_fillmd1_core()
141 else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) qpos += oplen; in bam_fillmd1_core()