
<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype = data/karyotype.txt

<image>
dir   = .
file  = binlinks-07.png
24bit = yes
#png = yes
#svg = yes
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
#angle_orientation = counterclockwise

auto_alpha_colors = yes
auto_alpha_steps  = 5
</image>

chromosomes_units           = 1000000

chromosomes_display_default = yes

#chromosomes = hs1;hs2

<highlights>
show = no
<highlight>
file = data/highlight.0.txt
r0   = 1.02r
r1   = 1.05r
</highlight>

<highlight>
show = no
file = data/highlight.1.txt
r0   = 1.1r
r1   = 1.125r
</highlight>

</highlights>

<plots>

<plot>
show = no
file = data/histogram.3.txt
type = histogram
r0   = 1.001r
r1   = 1.001r+200p
fill_under = yes
fill_color = black
max_gap = 5u
</plot>

<plot>
show = no
file = data/histogram.4.txt
type = histogram
r0   = 1.001r+250p
r1   = 1.001r+450p
fill_under = yes
fill_color = red
max_gap = 5u
</plot>

<plot>
show = no
file = data/histogram.5.txt
fill_under = yes
fill_color = chrx,chry,chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22
type = histogram
r0   = 1.06r
r1   = 1.06r+300p
color = black
thickness = 1p
sort_bin_values = yes
</plot>

<plot>
show = yes
file = data/histogram.6.txt
fill_under = yes
fill_color = chr4,chr8,chr15
type = histogram
r0   = 1.06r
r1   = 1.06r+300p
color = black
thickness = 1p
#sort_bin_values = yes
</plot>

</plots>

<links>
<link segdup>
show = yes
file = data/segdup.links.filtered.sorted.txt
ribbon = yes
color = black_a5
bezier_radius = 0r
bezier_radius_purity = 0.4
radius = 0.999r
<rules>
<rule>
importance = 100
condition  = 1
color      = eval("chr".substr(_CHR2_,2)."_a3")
</rule>
</rules>	
</link>
</links>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

units_ok = bupr
units_nounit = n

#debug_group = ticks
