Lines Matching refs:oplen
79 int j, oplen = cigar[i]>>4, op = cigar[i]&0xf; in bam_fillmd1_core() local
81 for (j = 0; j < oplen; ++j) { in bam_fillmd1_core()
96 if (j < oplen) break; in bam_fillmd1_core()
97 rpos += oplen; qpos += oplen; in bam_fillmd1_core()
101 for (j = 0; j < oplen; ++j) { in bam_fillmd1_core()
107 if (j < oplen) break; in bam_fillmd1_core()
109 qpos += oplen; in bam_fillmd1_core()
110 if (op == BAM_CINS) nm += oplen; in bam_fillmd1_core()
112 rpos += oplen; in bam_fillmd1_core()
123 int j, oplen = cigar[i]>>4, op = cigar[i]&0xf; in bam_fillmd1_core() local
125 for (j = 0; j < oplen; ++j) { in bam_fillmd1_core()
136 if (j < oplen) break; in bam_fillmd1_core()
137 rpos += oplen; qpos += oplen; in bam_fillmd1_core()
138 } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) rpos += oplen; in bam_fillmd1_core()
139 else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) qpos += oplen; in bam_fillmd1_core()