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52
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1
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2 # This is the main configuration file for the Circos tableviewer. This file also
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3 # depends on colors.conf (definition on basic colors), ideogram.conf (size and spacing of
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4 # row/cell segments), and ticks.conf (tick spacing and label definitions - these are turned
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5 # off by default).
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6 #
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7 # In addition to these configuration files, the bin/make-conf script creates
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8 # colors.conf (colors of row/col segments) and colors_percentile.conf (colors based on
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9 # cell percentile values). These configuration files are also included via the <<include>> directive.
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10 #
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11 # Some elements of the output image are toggled off by default (e.g. row and column highlights,
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12 # anchor links to segment labels, tick marks).
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13
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14 <colors>
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15 <<include DATA_DIR/etc_colors.conf>>
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16 <<include DATA_DIR/colors.conf>>
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17 <<include DATA_DIR/colors_percentile.conf>>
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18 </colors>
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19
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20 <fonts>
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21 <<include DATA_DIR/fonts.conf>>
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22 </fonts>
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23
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24 <<include DATA_DIR/ideogram.conf>>
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25 <<include DATA_DIR/ticks.conf>>
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26
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27 karyotype = DATA_DIR/karyotype.txt
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28
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29 <image>
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30 dir = DATA_DIR
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31 file = circos.png
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32 24bit = yes
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33 svg = yes
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34 png = yes
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35 # radius of inscribed circle in image
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36 radius = 1500p
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37 background = white
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38 # by default angle=0 is at 3 o'clock position
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39 angle_offset = -180
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40 auto_alpha_colors = yes
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41 auto_alpha_steps = 5
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42 </image>
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43
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44 chromosomes_units = 10
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45 chromosomes_display_default = yes
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46 chromosomes_order_by_karyotype = yes
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47
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48 <highlights>
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49
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50 show = yes
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51
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52 <highlight>
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53 show = no
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54 file = DATA_DIR/row.txt
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55 r0 = 1r+200p
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56 r1 = 1r+220p
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57 stroke_color = black
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58 stroke_thickness = 2
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59 </highlight>
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60
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61 <highlight>
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62 show = no
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63 file = DATA_DIR/col.txt
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64 r0 = 1r+230p
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65 r1 = 1r+250p
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66 stroke_color = black
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67 stroke_thickness = 2
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68 </highlight>
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69
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70 <highlight>
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71 show = no
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72 file = DATA_DIR/all.txt
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73 r0 = 1r+10p
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74 r1 = 1r+35p
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75 stroke_color = black
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76 stroke_thickness = 2
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77 </highlight>
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78
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79 </highlights>
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80
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81 <plots>
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82
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83 <plot>
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84 type = text
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85 file = DATA_DIR/segmentlabel.txt
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86 label_font = condensedbold
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87 color = black
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88 label_size = 30p
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89 r0 = 1r+50p
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90 r1 = 1r+500p
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91 rpadding = 0p
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92 padding = 0p
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93
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94 show_links = no
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95 link_dims = 0p,10p,32p,10p,5p
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96 link_thickness = 3p
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97 link_color = black
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98
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99 label_snuggle = no
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100 # shift label up to its height in pixels in the angular direction
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101 max_snuggle_distance = 2r
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102 snuggle_sampling = 2
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103 snuggle_tolerance = 0.25r
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104
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105 </plot>
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106
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107 </plots>
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108
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109 <links>
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110
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111 <link cellvalues>
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112 ribbon = yes
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113 flat = yes
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114 file = DATA_DIR/cells.txt
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115 bezier_radius = 0.0r
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116 radius = 0.999r-15p
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117 thickness = 1
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118 color = grey
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119 stroke_color = black
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120 stroke_thickness = 1
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121 <rules>
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122
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123 <rule>
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124 importance = 95
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125 condition = 1
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126 radius1 = 0.999r+2p
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127 flow = continue
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128 </rule>
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129
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130 </rules>
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131
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132 </link>
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133
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134 </links>
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135
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136 #anglestep = 0.5
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137 #minslicestep = 10
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138 #beziersamples = 40
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139 #debug = no
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140 #warnings = no
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141 #imagemap = no
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142
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143 #units_ok = bupr
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144 #units_nounit = n
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145
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146 <<include DATA_DIR/housekeeping.conf>>
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147
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