# circos.conf

karyotype = CRI-karyotype.txt

#below are the outset sections which I'm not going to do yet
#They would also have to be defined in the karyotype file

#chromosomes_radius  = dq1:1.1r,dq2:1.1r,dq3:1.1r,dq4:1.1r

<links>

################## Publications
<link>
file = pub.links
radius = 0.97r
bezier_radius = 0.3r
color = chr5
thickness = 6
#ribbon = yes
flat = yes
<rules>
<rule>
condition = 1
z          = eval(int(max(var(size1),var(size2))/100))
</rule>
</rules>
</link>
</links>



<ideogram>

<spacing>
default = 0.0005r
</spacing>

radius    = 0.65r
thickness = 150p
fill      = yes

show_label = yes
label_font = bold
label_size = 40
label_case = upper
label_radius = 1r + 50p
label_parallel = no
label_color = lyellow

</ideogram>

background = black

# <backgrounds>
# show  = data
# color = black
# </backgrounds>


################################################################
# The remaining content is standard and required. It is imported 
# from default files in the Circos distribution.
#
# These should be present in every Circos configuration file and
# overridden as required. To see the content of these files, 
# look in etc/ in the Circos distribution.

<image>
# Included from Circos distribution.
<<include etc/circos/image.conf>>
</image>

# RGB/HSV color definitions, color lists, location of fonts, fill patterns.
# Included from Circos distribution.
<<include etc/circos/colors_fonts_patterns.conf>>

# Debugging, I/O an dother system parameters
# Included from Circos distribution.
<<include etc/circos/housekeeping.conf>>
#track_defaults* = undef