# KARYOTYPE

karyotype =#KARYOTYPE

# CHROMOSOMES 
chromosomes_units = 1000

# LINKS BETWEEN AREAS BLAT
<links>

z      = 0
radius = 0.64r
crest  = 0.5
bezier_radius        = 0.25r
bezier_radius_purity = 1

<link>
z            = 20
color        = red
thickness    = 3
file         = #BLATLINKS_F
record_limit = #LINKSNUMBER_F
</link>
</links>

<link>
z            = 20
color        = green
thickness    = 3
file         = #BLATLINKS_R
record_limit = #LINKSNUMBER_R
</link>
</links>


# PLOTS
<plots>

# PLOT OF GENES' NAMES
<plot>
type  = text
color = red
file  = #FILEBANDS

r0    = 1r
r1    = 1r+300p

label_size = 40
label_font = condensed

show_links     = yes
link_dims      = 0p,2p,6p,2p,5p
link_thickness = 2p
link_color     = black

label_snuggle        = yes
max_snuggle_distance = 1r
snuggle_tolerance    = 0.25r
snuggle_sampling     = 2
snuggle_refine       = yes
</plot>

# PLOT OF SOFCLIPP NUMBER BY POSITION
<plot>
type = line
thickness = 8 #epaisseur
file = #SCFILE
min  = 0
max  = 1.0
r1   = 0.64r
r0   = 0.44r
color = vdred
fill_color = dred
extend_bin = no
orientation = in
</plot>

# PLOT OF DEPTH
<plot>
type = line
thickness = 4
file = #DATACOV
r1   = 0.82r
r0   = 0.66r
color = blue
fill_color = chr16
extend_bin = no
orientation = in
</plot>

<plot>
type = line
thickness = 4
file = #DATAMEDIANE
r1   = 0.82r
r0   = 0.66r
color = chr14
extend_bin = no
orientation = in
</plot>

# PLOT FREQUENCE
<plot>
type = line
thickness = 6
file = #DATAFREQ
min  = 0
max  = 1
r1   = 0.98r 
r0   = 0.82r 
color = black 
extend_bin = no

<backgrounds>
show  = data
<background>
color = vvvlgrey
</background>
<background>
color = vvlgrey
y0    = 0.25r
y1    = 0.50r
</background>
<background>
color = vlgrey
y0    = 0.50r
y1    = 0.75r
</background>
<background>
color = lgrey
y0    = 0.75r
</background>

</backgrounds>
</plot>
</plots>

<<include #IDEOGRAM>>
<<include #TICKS>>
<image>
dir = #NAMEDIR
file = #NAMEFILE
png = yes
svg = no
radius = 1500p
angle_offset = -90
auto_alpha_colors = yes
auto_alpha_steps  = 5
</image>

<<include colors_fonts_patterns.conf>> 
<<include housekeeping.conf>> 
