X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fbamcheck.c;h=b64c1690392bdf0bb1cca604c422f77df4fca9ca;hb=7c3295ba455fdc9269156dd1246c92ea5df3efd4;hp=352db21b12dbaf0edaa1a5d90f2e872aa258874f;hpb=60e0a8467ddbd0b89f15d201dcfe10c8796552b2;p=samtools.git

diff --git a/misc/bamcheck.c b/misc/bamcheck.c
index 352db21..b64c169 100644
--- a/misc/bamcheck.c
+++ b/misc/bamcheck.c
@@ -963,8 +963,8 @@ void output_stats(stats_t *stats)
     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);