Drop empty bins from coverage distribution

[samtools.git] / misc / bamcheck.c

diff --git a/misc/bamcheck.c b/misc/bamcheck.c
index a438adac3453e73a86f65017bb72ca54ba3ac4c4..d72e8008d9d1eb84810406a3a7bec15c1b7542a0 100644 (file)
--- a/misc/bamcheck.c
+++ b/misc/bamcheck.c
@@ -1050,12 +1050,14 @@ void output_stats(stats_t *stats)
     }
 
     printf("# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.\n");
-    printf("COV\t[<%d]\t%d\t%ld\n",stats->cov_min,stats->cov_min-1, (long)stats->cov[0]);
+    if  ( stats->cov[0] )
+        printf("COV\t[<%d]\t%d\t%ld\n",stats->cov_min,stats->cov_min-1, (long)stats->cov[0]);
     int icov;
     for (icov=1; icov<stats->ncov-1; icov++)
-        printf("COV\t[%d-%d]\t%d\t%ld\n",stats->cov_min + (icov-1)*stats->cov_step, stats->cov_min + icov*stats->cov_step-1,stats->cov_min + icov*stats->cov_step-1, (long)stats->cov[icov]);
-    printf("COV\t[%d<]\t%d\t%ld\n",stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov_min + (stats->ncov-2)*stats->cov_step-1, (long)stats->cov[stats->ncov-1]);
-
+        if ( stats->cov[icov] )
+            printf("COV\t[%d-%d]\t%d\t%ld\n",stats->cov_min + (icov-1)*stats->cov_step, stats->cov_min + icov*stats->cov_step-1,stats->cov_min + icov*stats->cov_step-1, (long)stats->cov[icov]);
+    if ( stats->cov[stats->ncov-1] )
+        printf("COV\t[%d<]\t%d\t%ld\n",stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov_min + (stats->ncov-2)*stats->cov_step-1, (long)stats->cov[stats->ncov-1]);
 
     // Calculate average GC content, then sort by GC and depth
     printf("# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n");