--- a/report_clonality/circos/circos.conf	Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/circos/circos.conf	Thu Feb 25 13:36:15 2021 +0000
@@ -1,147 +1,147 @@
-
-# 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   = yes
-png   = yes
-# 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>>
-
+
+# 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   = yes
+png   = yes
+# 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>>
+