FAQ

Q1. I get an error when producing the SVG files (e.g. Ubuntu 14.04). E.g. "Can't use an undefined value as an ARRAY reference at /usr/local/lib/perl5/site_perl/5.10.0/GD/SVG.pm line 1120."

A: "Get more recent versions of the GD and GD::SVG [perl] libraries and the problem will be solved. I am using GD 2.39 and GD::SVG 0.33"
--Lincoln D. Stein

A: Alexie:
I still have these issues with GD 2.56 and GD::SVG 0.33 (Ubuntu 14.04)
ERROR, thread [..] exited with error Can't use an undefined value as an ARRAY reference at /usr/local/share/perl/5.18.2/GD/SVG.pm line 1120, <STATSIN> line 2."
Troubleshooting:
It seems that Bio::Graphics::Glyph::xyplot::_draw_boxes makes a call to GD::SVG with a very high integer value
*1073742019 at /usr/local/share/perl/5.14.2/GD/SVG.pm line 1120.*
    GD::SVG::Image::_get_color('GD::SVG::Image=HASH(0x39be900)',
The problem seems to lie here:
  # Make the boxes transparent
  my $positive = $self->pos_color + 1073741824;
  my $negative = $self->neg_color + 1073741824;

What is the purpose of adding 1073741824 ? There isn't an color index above 200 when i dump the GD object. It seems that this integer addition is 
mainly for PNG formats and transparency? If I remove this addition, then the SVG works fine and the image is correct
[Reported gmod-devel-request@lists.sourceforge.net  19/05/2014. No reply]

Therefore solution:
edit
Bio/Graphics/Glyph/xyplot.pm
And add ;# as below at line 314 and 315 to remove the addition of this integer
  my $positive = $self->pos_color;# + 1073741824;
  my $negative = $self->neg_color;# + 1073741824;

Q2. I have a mix of single and pair ends. What shall I do?
A: Add the single ends as -1read but after all the paired end data. The program will say:
"Number of files for second readset does not equal to number of 1st readset. Extra files will be treated as single end readsets."