39 static void SetCigOp( CigOps * dst, char op, uint32_t oplen )  in SetCigOp()  argument
42     dst->oplen = oplen;  in SetCigOp()
605                 int avail_oplen = refOp[ ri - 1 ].oplen - ref_cop.oplen;  in CombineCIGAR()
610                         ref_cop.oplen -= delta;  in CombineCIGAR()
615                         ref_cop.oplen += avail_oplen;  in CombineCIGAR()
624                     ref_cop.oplen =0;   in CombineCIGAR()
629                 SetCigOp( &ref_cop, '=', ref_cop.oplen - delta );  in CombineCIGAR()
634         if ( ref_cop.oplen == 0 )  in CombineCIGAR()
637             if ( ref_cop.oplen == 0 )  in CombineCIGAR()
641             assert( ref_cop.oplen > 0 );  in CombineCIGAR()
646             if ( delta >=  ref_cop.oplen )  in CombineCIGAR()
648                 delta -= ref_cop.oplen * ref_cop.ref_sign;  in CombineCIGAR()
649                 ref_cop.oplen = 0;  in CombineCIGAR()
653                 ref_cop.oplen -= delta;  in CombineCIGAR()
662         if ( seq_cop.oplen == 0 )  in CombineCIGAR()
667                 assert( seq_cop.oplen > 0 );  in CombineCIGAR()
668                 seq_pos += seq_cop.oplen * seq_cop.seq_sign;  in CombineCIGAR()
678             int seq_seq_step = seq_cop.oplen * seq_cop.seq_sign; /** sequence movement**/  in CombineCIGAR()
679 …int seq_ref_step = seq_cop.oplen * seq_cop.ref_sign; /** influence of sequence movement on interme…  in CombineCIGAR()
680 …int ref_seq_step = ref_cop.oplen * ref_cop.seq_sign; /** movement of the intermediate reference **…  in CombineCIGAR()
681 …int ref_ref_step = ref_cop.oplen * ref_cop.ref_sign; /** influence of the intermediate reference m…  in CombineCIGAR()
685                 MACRO_BUILD_CIGAR( seq_cop.op, seq_cop.oplen );  in CombineCIGAR()
686                 seq_cop.oplen = 0;  in CombineCIGAR()
693                     MACRO_BUILD_CIGAR( ref_cop.op,ref_cop.oplen);  in CombineCIGAR()
694                     ref_cop.oplen = 0;  in CombineCIGAR()
698                     int min_len = ( seq_cop.oplen < ref_cop.oplen ) ? seq_cop.oplen : ref_cop.oplen;  in CombineCIGAR()
707                     seq_cop.oplen -= min_len;  in CombineCIGAR()
708                     ref_cop.oplen -= min_len;  in CombineCIGAR()
714                 int min_len = ( seq_cop.oplen < ref_cop.oplen ) ? seq_cop.oplen : ref_cop.oplen;  in CombineCIGAR()
720                         ref_cop.oplen -= min_len;  in CombineCIGAR()
721                         seq_cop.oplen -= min_len;  in CombineCIGAR()
726                         seq_cop.oplen -= min_len;  in CombineCIGAR()
732                     ref_cop.oplen -= min_len;  in CombineCIGAR()
739                     ref_cop.oplen -= min_len;  in CombineCIGAR()
740                     seq_cop.oplen -= min_len;  in CombineCIGAR()
1640             uint32_t op_len = cigops[ op_idx ].oplen;  in discover_rna_splicing_candidates()
1685 …rc = string_printf( &cigar[ dst ], cigar_len + 1 - dst, &sz, "%u%c", cigops[ idx ].oplen, cigops[ …  in change_rna_splicing_cigar()