printf("SN\treads QC failed:\t%ld\n", (long)stats->nreads_QCfailed);
printf("SN\tnon-primary alignments:\t%ld\n", (long)stats->nreads_secondary);
printf("SN\ttotal length:\t%ld\n", (long)stats->total_len);
- printf("SN\tbases mapped:\t%ld\n", (long)stats->nbases_mapped);
- printf("SN\tbases mapped (cigar):\t%ld\n", (long)stats->nbases_mapped_cigar);
+ printf("SN\tbases mapped:\t%ld\n", (long)stats->nbases_mapped); // the length of the whole read goes here, including soft-clips etc.
+ printf("SN\tbases mapped (cigar):\t%ld\n", (long)stats->nbases_mapped_cigar); // only matched and inserted bases are counted here
printf("SN\tbases trimmed:\t%ld\n", (long)stats->nbases_trimmed);
printf("SN\tbases duplicated:\t%ld\n", (long)stats->total_len_dup);
printf("SN\tmismatches:\t%ld\n", (long)stats->nmismatches);