## Include these first so that we can override defaults
<<include etc/housekeeping.conf>>
<<include etc/colors_fonts_patterns.conf>>

karyotype = data/karyotype.txt

## Global settings
chromosomes_units*	= 1000000
chromosomes_display_default* = yes

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

units_ok* = bupr
units_nounit* = n

<colors>
  #special colors 
  IS1   = 255,38,0
  IS186 = 0,143,0
  IS3   = 4,51,255 
  IS150 = 250,167,87
  IS911 = 1,0,0
  IS4   = 123,25,121
  IS2   = 102,161,221
  IS30  = 97,115,53
  IS600 = 178,126,0
</colors>

<ideogram>

	<spacing>
	
		default = 0u
		break   = 0u
		
		axis_break_at_edge = no
		axis_break         = no
	
	</spacing>
	
	# thickness (px) of chromosome ideogram
	thickness        = 1p
	stroke_thickness = 0p
	# ideogram border color
	stroke_color     = white
	fill             = yes
	# the default chromosome color is set here and any value defined in the karyotype file overrides it
	fill_color       = black
	
	# fractional radius position of chromosome ideogram within image 
	radius         = ind_scale #0.7r
	show_label     = no
	label_with_tag = yes
	label_color    = black
	label_font     = condensedbold
	label_radius   = 0.01r
	label_size     = 24
	label_parallel = yes
	label_center   = yes
	
	# show_bands determines whether the outline of cytogenetic bands will be seen
	show_bands            = no
	# in order to fill the bands with the color defined in the karyotype file you must set fill_bands
	fill_bands            = no

</ideogram>
<image>
	svg = yes
	dir = ./
	file = mobs.png
	# radius of inscribed circle in image
	radius         = 400p
	background     = white
	# by default angle=0 is at 3 o'clock position
	angle_offset   = -90
</image>

show_ticks          = yes
show_tick_labels    = yes

<ticks>

	chromosomes_display_default = yes
	
	chromosomes = REL606
	
	radius               = 1r
	orientation          = in
	label_multiplier     = 1e-6
	
	<tick>
		spacing        = 100000b
		size           = 5p
		thickness      = 2p
		color          = black
		show_label     = no
	</tick>
	
	<tick>
		spacing		= 500000b
		size 		= 10p
		thickness 	= 4p
		color 		= black
		show_label 	= yes
		label_size	= 24p
		label_offset	= 3p
		label_rotate	= yes
		format		= %.1f Mb
		skip_first_label = no
	</tick>

</ticks>

<plots>
	<plot>
		show = yes
		
		type = line
		file = data/empty_data.txt
		
		glyph = circle
		glyph_size = 8
		
		fill_color = blue
		stroke_color = blue
		stroke_thickness = 1
		
		min = 3
		max = 3.01
		
		r0 = ind_syn_axis_value_1
		r1 = ind_syn_axis_value_2
		axis = yes
		axis_color = black
		axis_thickness = 1
		axis_spacing = 1
	</plot>
	
	<plot>
		show = yes
		
		type = line
		file = data/empty_data.txt
		
		glyph = circle
		glyph_size = 8
		
		fill_color = blue
		stroke_color = blue
		stroke_thickness = 1
		
		min = 3
		max = 3.01
		
		r0 = ind_nonsyn_axis_value_1
		r1 = ind_nonsyn_axis_value_2
		axis = yes
		axis_color = black
		axis_thickness = 1
		axis_spacing = 1
	</plot>
	
	<plot>
		label_font = glyph
		label_size = mob_value #20p
		label_snuggle = no
		
		show = yes
		
		type  = text
		file  = data/mobs_data.txt
		
		stroke_thickness = 5
		stroke_color = black
		
		r0 = 1r
		r1 = 2r
		
		padding = -100p
		rpadding = 0p

		label_rotate = no
		
		<rules>
			<rule>
				importance = 100
				condition = eval( _VALUE_ eq "ileft")
				value = eval("\x69")
			</rule>
			<rule>
				importance = 90
				condition = eval( _VALUE_ eq "iright")
				value = eval("\x6C")
			</rule>
			<rule>
				importance = 80
				condition = eval( _VALUE_ eq "oleft")
				value = eval("\x69")
				rpadding = space_value_in_pixels
			</rule>
			<rule>
				importance = 70
				condition = eval( _VALUE_ eq "oright")
				value = eval("\x6C")
				rpadding = space_value_in_pixels
			</rule>
		</rules>
	</plot>
	

</plots>

