295     uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0;  in bam_trim_left()  local
344                 qry_removed += bam_cigar_oplen(orig_cigar[i]);  in bam_trim_left()
357             qry_removed += ref_remove;  in bam_trim_left()
360         qry_removed = rec->core.l_qseq;  in bam_trim_left()
364     if (clipping == hard_clip && hardclip + qry_removed > 0) {  in bam_trim_left()
365         new_cigar[j++] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP);  in bam_trim_left()
371         if (qry_removed > 0) {  in bam_trim_left()
372             new_cigar[j++] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP);  in bam_trim_left()
391         qry_removed = 0; // Copy all the sequence and confidence values  in bam_trim_left()
395     new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2;  in bam_trim_left()
397     if ((qry_removed & 1) == 0) {  in bam_trim_left()
398         memcpy(bam_get_seq(rec_out), orig_seq + (qry_removed / 2),  in bam_trim_left()
399                 (rec->core.l_qseq - qry_removed + odd_base) / 2);  in bam_trim_left()
401         uint8_t *in = orig_seq + qry_removed / 2;  in bam_trim_left()
404         for (i = qry_removed; i < rec->core.l_qseq - 1; i += 2) {  in bam_trim_left()
415     memmove(new_qual, orig_qual, rec->core.l_qseq - qry_removed);  in bam_trim_left()
418     rec_out->core.l_qseq -= qry_removed;  in bam_trim_left()
446     uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0;  in bam_trim_right()  local
492                 qry_removed += bam_cigar_oplen(orig_cigar[i]);  in bam_trim_right()
500             qry_removed += ref_remove;  in bam_trim_right()
503         if (qry_removed > 0) j++;  in bam_trim_right()
504         if (hardclip > 0 && (clipping == soft_clip || qry_removed == 0)) j++;  in bam_trim_right()
506         qry_removed = rec->core.l_qseq;  in bam_trim_right()
511     if (clipping == hard_clip && hardclip + qry_removed > 0) {  in bam_trim_right()
512         new_cigar[j] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP);  in bam_trim_right()
519             if (qry_removed > 0) --j;  in bam_trim_right()
521         if (qry_removed > 0) {  in bam_trim_right()
522             new_cigar[j] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP);  in bam_trim_right()
541         qry_removed = 0; // Copy all the sequence and confidence values  in bam_trim_right()
543     new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2;  in bam_trim_right()
545     memcpy(bam_get_seq(rec_out), orig_seq, (rec->core.l_qseq - qry_removed + 1) / 2);  in bam_trim_right()
548     memcpy(new_qual, orig_qual, rec->core.l_qseq - qry_removed);  in bam_trim_right()
551     rec_out->core.l_qseq -= qry_removed;  in bam_trim_right()