## 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

<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 #0.70r
	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 = indels.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
	
	orientation          = in
	label_multiplier     = 1e-6
	
	<tick>
		spacing        = 100000b
		size           = 5p
		thickness      = 2p
		color          = black
		show_label     = no
		radius = 1r
	</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
		radius = 1r
	</tick>

</ticks>

<plots>
	<plot>
		show  = yes
		type  = tile
		file  = data/indels_data.txt
		
		layers = 1
		layers_overflow = grow
		
		stroke_thickness = 1
		stroke_color = black
		
		margin = 0.005u
		orientation = out
		
		thickness = indel_value
		padding = 4p
		
		r0 = 1.01r
		r1 = 2r
		
		background = no
	</plot>
</plots>

