New --GC-depth option to bamcheck. Take into account not so frequent CIGAR codes...

[samtools.git] / misc / plot-bamcheck

diff --git a/misc/plot-bamcheck b/misc/plot-bamcheck
index d5857f15798d25995913f4f517048a88c4d64ef0..1792c6ffe8c0647b640a075f301f6e6cd7293c5d 100755 (executable)
--- 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};