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# Field delimiter specifies the assignment operator, e.g.
30
34
list_field_delim = \s*[:=]\s*
36
# Rule fields and other parameters accept var(VARIABLE) syntax
37
# to reference parameters of data points. By default, if
38
# VARIABLE does not exist, Circos quits with an error, unless
39
# the skip parameter below is set.
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# This feature is useful when you have data that don't always
42
# have the same options. For example,
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skip_missing_expression_vars = no
32
48
# Magnification factor for text in SVG files.
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svg_font_scale = 1.3
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# default font - pick one of the keys from <fonts> block
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default_font = default
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# default font name is used for SVG files for cases where
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# the font definition does not include a name
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# see etc/fonts.conf for details
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default_font_name = Arial
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default_font_color = black
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# default color for cases when color is not specified
35
76
# Receive debug messages about actions
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78
# Comma-separated list of one or more of the following
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105
# parameters passed to functions can be
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106
# validated to check consistency. turn this
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107
# off to speed things up
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# Reformat numbers in debug output for consistency.
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# If you have a lot of debug output (e.g. -debug_group _all)
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# this will slow things considerably.
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debug_output_tidy = no
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115
# pixel sub-sampling for text tracks
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text_pixel_subsampling = 1
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# array or span - use 'span' if applying snuggle refinement
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118
text_snuggle_method = array
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# restrict names of parameters?
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# if 'yes' then only certain named parameters are allowed within
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# blocks and option fields for data
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# if 'no' then you can define parameters with any name what-so-ever,
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# useful if you wish to define states or labels for your data
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# e.g. hs1 10 20 0.5 paired=yes,special=no,myvar=0.5
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# ordinarily, 'paired', 'special' and 'myvar' would not be allowed
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restrict_parameter_names = yes
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# The location of configuration and data files will be guessed if
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# (a) configuration file is not specified
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# (b) data file paths are relative
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# Circos will look in the following locations, where
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# SCRIPTPATH is the location of the 'circos' script (e.g. /usr/local/bin) and
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# CWD is the current directory (where the 'circos' command was executed).
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# All paths under CWD will be scanned first, then under SCRIPTPATH.
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# {CWD,SCRIPTPATH}/..
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# {CWD,SCRIPTPATH}/etc/
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# {CWD,SCRIPTPATH}/../etc
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# {CWD,SCRIPTPATH}/../../etc
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# {CWD,SCRIPTPATH}/data
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# {CWD,SCRIPTPATH}/../data
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# {CWD,SCRIPTPATH}/../../data
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# If you would like to prepend this list with custom directories for
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# data files, enter them as a CSV list here
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# data_path = /home/martink/circos-tutorials
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# If the cache is static, it will always be used and will not be updated
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# unless it is deleted (use -color_cache_rebuild on the command line).
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# Otherwise, the cache will be updated if
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# - config file is newer than cache file
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# - list of colors in config file is different than in cache file
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color_cache_static = no
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color_cache_file = circos.colorlist
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# if the directory is not defined, then the system will guess a temporary
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# directory compatible with your operating system (using File::Temp)
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# color_cache_dir = /tmp
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# Make some functions faster. This should always be 'yes' unless you
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# want things to run slowly or suspect deep issues.
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# This is a debugging flag and should be set to 'no' for regular use
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# Number of iterations for determining ideogram sizes when
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# relative scale is used.
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relative_scale_iterations = 10
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# min, max, average, mode - based on scale statistics of ALL ideograms
176
# minadj, maxadj, averageadj, modeadj - based on scale statistics of adjacent ideograms
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# You can specify a fixed scale for spacing using a floating value
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# e.g. relative_scale_spacing = 1.5
181
relative_scale_spacing = mode
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# What to do with out-of-range data. Either 'clip' or 'hide'
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data_out_of_range = clip
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# Track default directory
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track_defaults = etc/tracks
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# Use anti aliasing, where possible? I've seen bugs in some gd libraries
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# that cause artefacts to appear when lines are anti-aliased. If your
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# image contains unexpected elements, turn aa off.
added
removed
etc/housekeeping.conf
