--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/report_clonality/circos/circos.conf	Mon Aug 29 05:41:20 2016 -0400
@@ -0,0 +1,148 @@
+
+# This is the main configuration file for the Circos tableviewer. This file also
+# depends on colors.conf (definition on basic colors), ideogram.conf (size and spacing of
+# row/cell segments), and ticks.conf (tick spacing and label definitions - these are turned
+# off by default).
+#
+# In addition to these configuration files, the bin/make-conf script creates 
+# colors.conf (colors of row/col segments) and colors_percentile.conf (colors based on
+# cell percentile values). These configuration files are also included via the <<include>> directive.
+#
+# Some elements of the output image are toggled off by default (e.g. row and column highlights, 
+# anchor links to segment labels, tick marks).
+
+<colors>
+<<include DATA_DIR/etc_colors.conf>>
+<<include DATA_DIR/colors.conf>>
+<<include DATA_DIR/colors_percentile.conf>>
+</colors>
+
+<fonts>
+<<include DATA_DIR/fonts.conf>>
+</fonts>
+
+<<include DATA_DIR/ideogram.conf>>
+<<include DATA_DIR/ticks.conf>>
+
+karyotype = DATA_DIR/karyotype.txt
+
+<image>
+dir   = DATA_DIR
+file  = circos.png
+24bit = yes
+svg   = no
+png   = yes
+pdf   = no
+# radius of inscribed circle in image
+radius         = 1500p
+background     = white
+# by default angle=0 is at 3 o'clock position
+angle_offset   = -180
+auto_alpha_colors = yes
+auto_alpha_steps  = 5
+</image>
+
+chromosomes_units              = 10
+chromosomes_display_default    = yes
+chromosomes_order_by_karyotype = yes
+
+<highlights>
+
+show = yes
+
+<highlight>
+show = no
+file = DATA_DIR/row.txt
+r0 = 1r+200p
+r1 = 1r+220p
+stroke_color = black
+stroke_thickness = 2
+</highlight>
+
+<highlight>
+show = no
+file = DATA_DIR/col.txt
+r0 = 1r+230p
+r1 = 1r+250p
+stroke_color = black
+stroke_thickness = 2
+</highlight>
+
+<highlight>
+show = no
+file = DATA_DIR/all.txt
+r0 = 1r+10p
+r1 = 1r+35p
+stroke_color = black
+stroke_thickness = 2
+</highlight>
+
+</highlights>
+
+<plots>
+
+<plot>
+type = text
+file = DATA_DIR/segmentlabel.txt
+label_font = condensedbold
+color = black
+label_size = 30p
+r0   = 1r+50p
+r1   = 1r+500p
+rpadding = 0p
+padding = 0p
+
+show_links     = no
+link_dims      = 0p,10p,32p,10p,5p
+link_thickness = 3p
+link_color     = black
+
+label_snuggle             = no
+# shift label up to its height in pixels in the angular direction
+max_snuggle_distance      = 2r
+snuggle_sampling          = 2
+snuggle_tolerance         = 0.25r
+
+</plot>
+
+</plots>
+
+<links>
+
+<link cellvalues>
+ribbon        = yes
+flat          = yes
+file          = DATA_DIR/cells.txt
+bezier_radius = 0.0r
+radius        = 0.999r-15p
+thickness     = 1
+color         = grey
+stroke_color     = black
+stroke_thickness = 1
+<rules>
+
+<rule>
+importance = 95
+condition  = 1
+radius1    = 0.999r+2p
+flow       = continue
+</rule>
+
+</rules>
+
+</link>
+
+</links>
+
+#anglestep       = 0.5
+#minslicestep    = 10
+#beziersamples   = 40
+#debug           = no
+#warnings        = no
+#imagemap        = no
+
+#units_ok = bupr
+#units_nounit = n
+
+<<include DATA_DIR/housekeeping.conf>>
+