Merge remote branch 'remotes/pierre/master' into develop

[samtools.git] / misc / plot-bamcheck

diff --git a/misc/plot-bamcheck b/misc/plot-bamcheck
index adaebe6e92d218533925754758e7c46ba4e852b3..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};
@@ -803,14 +805,17 @@ sub plot_indel_cycles
         set style line 1 linetype 1  linecolor rgb "red"
         set style line 2 linetype 2  linecolor rgb "black"
         set style line 3 linetype 3  linecolor rgb "green"
+        set style line 4 linetype 4  linecolor rgb "blue"
         set style increment user
         set ylabel "Indel count" 
         set xlabel "Read Cycle"
         set title "$$args{title}"
-        plot '-' w l ti 'Insertions', '' w l ti 'Deletions'
+        plot '-' w l ti 'Insertions (fwd)', '' w l ti 'Insertions (rev)', '' w l ti 'Deletions (fwd)', '' w l ti 'Deletions (rev)'
     ];
     for my $len (@{$$opts{dat}{IC}}) { print $fh "$$len[0]\t$$len[1]\n"; } print $fh "end\n";
     for my $len (@{$$opts{dat}{IC}}) { print $fh "$$len[0]\t$$len[2]\n"; } print $fh "end\n";
+    for my $len (@{$$opts{dat}{IC}}) { print $fh "$$len[0]\t$$len[3]\n"; } print $fh "end\n";
+    for my $len (@{$$opts{dat}{IC}}) { print $fh "$$len[0]\t$$len[4]\n"; } print $fh "end\n";
     close($fh);
     plot($$args{gp});
 }