X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fplot-bamcheck;h=1792c6ffe8c0647b640a075f301f6e6cd7293c5d;hb=12c0954c689d82000572078a756678142f9a7826;hp=d5857f15798d25995913f4f517048a88c4d64ef0;hpb=973747517611624ac4a94db42ba210a3b181acac;p=samtools.git

diff --git a/misc/plot-bamcheck b/misc/plot-bamcheck
index d5857f1..1792c6f 100755
--- a/misc/plot-bamcheck
+++ b/misc/plot-bamcheck
@@ -349,6 +349,7 @@ sub plot_qualities
                 set size 0.4,0.8
                 unset ytics
                 set y2tics mirror
+				set yrange [0:$yrange]
                 unset ylabel
                 set xlabel "Cycle (rev reads)"
                 set label "$$args{title}" at screen 0.5,0.95 center
@@ -662,7 +663,8 @@ sub plot_coverage
 
     my @vals;
     for my $cov (@{$$opts{dat}{COV}}) { push @vals,$$cov[2]; }
-    my $p99 = percentile(99.8,@vals);
+    my $i = percentile(99.8,@vals);
+    my $p99 = $$opts{dat}{COV}[$i][1];
 
     my $args = get_defaults($opts,"$$opts{prefix}coverage.png");
     my $fh = $$args{fh};