Mercurial > repos > davidvanzessen > argalaxy_tools

annotate report_clonality/circos/housekeeping.conf @ 58:4c6df851e262 draft default tip

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"planemo upload commit 1a7731bb4fe2e80fb1fdc88121783068af3edb08"
author rhpvorderman
date Fri, 21 Apr 2023 10:04:39 +0000
parents 81b3eb11ed2c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
54
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1 # Housekeeping parameters, which must be included
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2 # at the top level of the configuration.
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3 #
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4 # Don't adjust these, unless you know what you are doing, or
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5 # feel like experimenting
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6
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7 anglestep = 0.5
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8 minslicestep = 10
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9 beziersamples = 40 # bezier curves are drawn piece-wise
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10 # linear, with this many samples
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11 debug = no
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12 warnings = no
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13 imagemap = no
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14 paranoid = yes
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15
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16 units_ok = bupr
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17 units_nounit = n
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18
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19 # \t tab
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20 # \s any whitespace
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21 file_delim = \s
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22 # collapse adjacent whitespace
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23 # e.g. two spaces are treated as one, not as a missing field
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24 file_delim_collapse = yes
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25
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26 # Record delimiter for parameter values that are lists, such as
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27 # hs1:0.25;hs2:0.10. By default, both ; and , are accepted
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28 #
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29 # e.g. hs1:0.25,hs2:0.10
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30 # hs1:0.25;hs2:0.10
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31 list_record_delim = \s*[;,]\s*
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32 # Field delimiter specifies the assignment operator, e.g.
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33 list_field_delim = \s*[:=]\s*]
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34
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35 # Rule fields and other parameters accept var(VARIABLE) syntax
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36 # to reference parameters of data points. By default, if
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37 # VARIABLE does not exist, Circos quits with an error, unless
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38 # the skip parameter below is set.
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39 #
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40 # This feature is useful when you have data that don't always
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41 # have the same options. For example,
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42 #
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43 # chr1 10 20 a=10
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44 # chr1 50 60 b=10
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45 skip_missing_expression_vars = no
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46
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47 # In old versions, data point parameters were referenced using _NAME_
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48 # syntax. This has been replaced with var(NAME). The _NAME_ syntax is
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49 # deprecated (for example, it will break when dealing with fields like
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50 # gene_a_1). If you must use it, set the parameter below.
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51
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52 legacy_underline_expression_syntax = no
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53
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54 # Magnification factor for text in SVG files.
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55 svg_font_scale = 1.3
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56
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57 # default font - pick one of the keys from <fonts> block
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58 default_font = default
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59 # default font name is used for SVG files for cases where
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60 # the font definition does not include a name
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61 # see etc/fonts.conf for details
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62 default_font_name = Arial
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63 default_font_color = black
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64
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65 # default color for cases when color is not specified
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66 default_color = black
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67
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68 <guides>
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69 thickness = 1
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70 size = 5
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71 type = outline
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72 <object>
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73 all = no
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74 ideogram = no
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75 ideogram_label = no
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76 </object>
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77 <color>
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78 default = lblue
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79 text = red
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80 </color>
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81 </guides>
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82
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83 # Receive debug messages about actions
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84 #
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85 # Comma-separated list of one or more of the following
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86 #
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87 # summary - top level indications of what's happening
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88 # chrfilter - ideogram filtering (parsing 'chromosomes' parameter)
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89 # conf - configuration file
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90 # counter - plot counters
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91 # spacing - ideogram spacing
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92 # scale - ideogram scaling
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93 # ideogram - ideogram reporting
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94 # anglepos - report angle positions for base pair coordinates
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95 # zoom - zoom regions
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96 # layers - specific plot z-layers
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97 # rules - dynamic rules
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98 # text - text tracks
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99 # heatmap - detailed heatmap reports
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100 # brush - brushes
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101 # color - color allocation and definition
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102 # ticks - tick marks and labels
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103 # timers - some benchmark timings
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104 # cache - caches
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105 # _all - turn on all groups
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106 debug_group = summary
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107
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108 # run length duration after which timing report is automatically
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109 # generated at the end of the run
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110 debug_auto_timer_report = 30
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111
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112 debug_word_separator = " "
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113 debug_undef_text = _undef_
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114 debug_empty_text = _emptylist_
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115
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116 # parameters passed to functions can be
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117 # validated to check consistency. turn this
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118 # off to speed things up
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119 debug_validate = yes
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120
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121 # Reformat numbers in debug output for consistency.
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122 # If you have a lot of debug output (e.g. -debug_group _all)
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123 # this will slow things considerably.
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124 debug_output_tidy = no
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125
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126 # pixel sub-sampling for text tracks
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127 text_pixel_subsampling = 1
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128 # array or span - use 'span' if applying snuggle refinement
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129 text_snuggle_method = array
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130
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131 # restrict names of parameters?
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132 # if 'yes' then only certain named parameters are allowed within
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133 # blocks and option fields for data
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134 #
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135 # if 'no' then you can define parameters with any name what-so-ever,
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136 # useful if you wish to define states or labels for your data
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137 #
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138 # e.g. hs1 10 20 0.5 paired=yes,special=no,myvar=0.5
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139 #
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140 # ordinarily, 'paired', 'special' and 'myvar' would not be allowed
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141 restrict_parameter_names = no
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142
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143 # Unless set to 'yes', parameter names will be converted to lowercase
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144 case_sensitive_parameter_names = no
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145
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146 # The location of configuration and data files will be guessed if
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147 # (a) configuration file is not specified
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148 # (b) data file paths are relative
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149 # Circos will look in the following locations, where
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150 # SCRIPTPATH is the location of the 'circos' script (e.g. /usr/local/bin) and
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151 # CWD is the current directory (where the 'circos' command was executed).
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152 # All paths under CWD will be scanned first, then under SCRIPTPATH.
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153 #
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154 # {CWD,SCRIPTPATH}/.
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155 # {CWD,SCRIPTPATH}/..
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156 # {CWD,SCRIPTPATH}/etc/
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157 # {CWD,SCRIPTPATH}/../etc
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158 # {CWD,SCRIPTPATH}/../../etc
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159 # {CWD,SCRIPTPATH}/data
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160 # {CWD,SCRIPTPATH}/../data
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161 # {CWD,SCRIPTPATH}/../../data
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162 #
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163 # If you would like to prepend this list with custom directories for
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164 # data files, enter them as a CSV list here
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165 # data_path = /home/martink/circos-tutorials
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166 # If the cache is static, it will always be used and will not be updated
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167 # unless it is deleted (use -color_cache_rebuild on the command line).
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168 # Otherwise, the cache will be updated if
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169 # - config file is newer than cache file
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170 # - list of colors in config file is different than in cache file
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171 color_cache_static = yes
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172 color_cache_file = circos.colorlist
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173 color_lists_use = yes
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174 # if the directory is not defined, then the system will guess a temporary
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175 # directory compatible with your operating system (using File::Temp)
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176 # color_cache_dir = /tmp
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177
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178 # Make some functions faster. This should always be 'yes' unless you
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179 # want things to run slowly or suspect deep issues.
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180 memoize = yes
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181
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182 # This is a debugging flag and should be set to 'no' for regular use
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183 quit_on_dump = yes
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184
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185 offsets = 0,0
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186
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187 # Maximum number of image and data elements. If these are exceeded,
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188 # Circos will quit with an error. These values are arbitrary, but in
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189 # my experience images with significantly more data points than this
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190 # are uninterpretable.
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191
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192 max_ticks = 5000
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193 max_ideograms = 200
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194 max_links = 25000
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195 max_points_per_track = 25000
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196
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197 # What to do when data is found for an ideogram that does not appear in the karyotype file.
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198
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199 # Set to 'skip' or 'exit'
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200 undefined_ideogram = skip
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201
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202 # Number of iterations for determining ideogram sizes when
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203 # relative scale is used.
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204 relative_scale_iterations = 10
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205
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206 # min, max, average, mode - based on scale statistics of ALL ideograms
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207 # minadj, maxadj, averageadj, modeadj - based on scale statistics of adjacent ideograms
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208 #
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209 # You can specify a fixed scale for spacing using a floating value
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210 #
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211 # e.g. relative_scale_spacing = 1.5
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212 relative_scale_spacing = mode
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213
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214 # What to do with out-of-range data. Either 'clip' or 'hide'
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215 data_out_of_range = clip
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216
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217 # Track default directory
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218 track_defaults = etc/tracks
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219
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220 # Use round brushes for elements with thickness greater than round_brush_min_thickness?
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221 round_brush_use = yes
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222 round_brush_min_thickness = 5
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223
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224 # Use anti aliasing, where possible? I've seen bugs in some gd libraries
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225 # that cause artefacts to appear when lines are anti-aliased. If your
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226 # image contains unexpected elements, turn aa off.
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227 anti_aliasing = yes
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228
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229 # A parameter that must be set. Checks whether this file was imported.
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230 housekeeping = yes