--- a/report_clonality/circos/housekeeping.conf	Thu Aug 08 07:40:36 2019 -0400
+++ b/report_clonality/circos/housekeeping.conf	Thu Feb 25 13:36:15 2021 +0000
@@ -1,230 +1,230 @@
-# Housekeeping parameters, which must be included
-# at the top level of the configuration.
-#
-# Don't adjust these, unless you know what you are doing, or
-# feel like experimenting
-
-anglestep       = 0.5
-minslicestep    = 10
-beziersamples   = 40 # bezier curves are drawn piece-wise
-                     # linear, with this many samples
-debug           = no
-warnings        = no
-imagemap        = no
-paranoid        = yes
-
-units_ok        = bupr
-units_nounit    = n
-
-# \t  tab
-# \s  any whitespace
-file_delim = \s
-# collapse adjacent whitespace
-# e.g. two spaces are treated as one, not as a missing field
-file_delim_collapse = yes
-
-# Record delimiter for parameter values that are lists, such as
-# hs1:0.25;hs2:0.10. By default, both ; and , are accepted
-#
-# e.g. hs1:0.25,hs2:0.10
-#      hs1:0.25;hs2:0.10
-list_record_delim = \s*[;,]\s*
-# Field delimiter specifies the assignment operator, e.g.
-list_field_delim  = \s*[:=]\s*]
-
-# Rule fields and other parameters accept var(VARIABLE) syntax
-# to reference parameters of data points. By default, if
-# VARIABLE does not exist, Circos quits with an error, unless
-# the skip parameter below is set.
-#
-# This feature is useful when you have data that don't always
-# have the same options. For example,
-#
-# chr1 10 20 a=10
-# chr1 50 60 b=10
-skip_missing_expression_vars = no
-
-# In old versions, data point parameters were referenced using _NAME_
-# syntax. This has been replaced with var(NAME). The _NAME_ syntax is
-# deprecated (for example, it will break when dealing with fields like
-# gene_a_1). If you must use it, set the parameter below.
-
-legacy_underline_expression_syntax = no
-
-# Magnification factor for text in SVG files.
-svg_font_scale = 1.3
-
-# default font - pick one of the keys from <fonts> block
-default_font   = default
-# default font name is used for SVG files for cases where
-# the font definition does not include a name
-# see etc/fonts.conf for details
-default_font_name  = Arial
-default_font_color = black
-
-# default color for cases when color is not specified
-default_color  = black
-
-<guides>
-thickness      = 1
-size           = 5
-type           = outline
-<object>
-all            = no
-ideogram       = no
-ideogram_label = no
-</object>
-<color>
-default = lblue
-text    = red
-</color>
-</guides>
-
-# Receive debug messages about actions
-#
-# Comma-separated list of one or more of the following
-#
-# summary   - top level indications of what's happening
-# chrfilter - ideogram filtering (parsing 'chromosomes' parameter)
-# conf      - configuration file
-# counter   - plot counters
-# spacing   - ideogram spacing
-# scale     - ideogram scaling
-# ideogram  - ideogram reporting
-# anglepos  - report angle positions for base pair coordinates
-# zoom      - zoom regions
-# layers    - specific plot z-layers
-# rules     - dynamic rules
-# text      - text tracks
-# heatmap   - detailed heatmap reports
-# brush     - brushes
-# color     - color allocation and definition
-# ticks     - tick marks and labels
-# timers    - some benchmark timings
-# cache     - caches
-# _all      - turn on all groups
-debug_group = summary
-
-# run length duration after which timing report is automatically
-# generated at the end of the run
-debug_auto_timer_report = 30
-
-debug_word_separator = " "
-debug_undef_text     = _undef_
-debug_empty_text     = _emptylist_
-
-# parameters passed to functions can be
-# validated to check consistency. turn this
-# off to speed things up
-debug_validate       = yes
-
-# Reformat numbers in debug output for consistency.
-# If you have a lot of debug output (e.g. -debug_group _all)
-# this will slow things considerably.
-debug_output_tidy    = no
-
-# pixel sub-sampling for text tracks
-text_pixel_subsampling = 1
-# array or span - use 'span' if applying snuggle refinement
-text_snuggle_method    = array
-
-# restrict names of parameters?
-# if 'yes' then only certain named parameters are allowed within
-# blocks and option fields for data
-#
-# if 'no' then you can define parameters with any name what-so-ever,
-# useful if you wish to define states or labels for your data
-#
-# e.g. hs1 10 20 0.5 paired=yes,special=no,myvar=0.5
-#
-# ordinarily, 'paired', 'special' and 'myvar' would not be allowed
-restrict_parameter_names = no
-
-# Unless set to 'yes', parameter names will be converted to lowercase
-case_sensitive_parameter_names = no
-
-# The location of configuration and data files will be guessed if
-# (a) configuration file is not specified
-# (b) data file paths are relative
-# Circos will look in the following locations, where
-# SCRIPTPATH is the location of the 'circos' script (e.g. /usr/local/bin) and
-# CWD is the current directory (where the 'circos' command was executed).
-# All paths under CWD will be scanned first, then under SCRIPTPATH.
-#
-# {CWD,SCRIPTPATH}/.
-# {CWD,SCRIPTPATH}/..
-# {CWD,SCRIPTPATH}/etc/
-# {CWD,SCRIPTPATH}/../etc
-# {CWD,SCRIPTPATH}/../../etc
-# {CWD,SCRIPTPATH}/data
-# {CWD,SCRIPTPATH}/../data
-# {CWD,SCRIPTPATH}/../../data
-#
-# If you would like to prepend this list with custom directories for
-# data files, enter them as a CSV list here
-# data_path = /home/martink/circos-tutorials
-# If the cache is static, it will always be used and will not be updated
-# unless it is deleted (use -color_cache_rebuild on the command line).
-# Otherwise, the cache will be updated if
-#  - config file is newer than cache file
-#  - list of colors in config file is different than in cache file
-color_cache_static = yes
-color_cache_file   = circos.colorlist
-color_lists_use    = yes
-# if the directory is not defined, then the system will guess a temporary
-# directory compatible with your operating system (using File::Temp)
-# color_cache_dir    = /tmp
-
-# Make some functions faster. This should always be 'yes' unless you
-# want things to run slowly or suspect deep issues.
-memoize = yes
-
-# This is a debugging flag and should be set to 'no' for regular use
-quit_on_dump = yes
-
-offsets = 0,0
-
-# Maximum number of image and data elements. If these are exceeded,
-# Circos will quit with an error. These values are arbitrary, but in
-# my experience images with significantly more data points than this
-# are uninterpretable.
-
-max_ticks            = 5000
-max_ideograms        = 200
-max_links            = 25000
-max_points_per_track = 25000
-
-# What to do when data is found for an ideogram that does not appear in the karyotype file.
-
-# Set to 'skip' or 'exit'
-undefined_ideogram = skip
-
-# Number of iterations for determining ideogram sizes when
-# relative scale is used.
-relative_scale_iterations = 10
-
-# min, max, average, mode             - based on scale statistics of ALL ideograms
-# minadj, maxadj, averageadj, modeadj - based on scale statistics of adjacent ideograms
-#
-# You can specify a fixed scale for spacing using a floating value
-#
-# e.g. relative_scale_spacing = 1.5
-relative_scale_spacing    = mode
-
-# What to do with out-of-range data. Either 'clip' or 'hide'
-data_out_of_range = clip
-
-# Track default directory
-track_defaults = etc/tracks
-
-# Use round brushes for elements with thickness greater than round_brush_min_thickness?
-round_brush_use           = yes
-round_brush_min_thickness = 5
-
-# Use anti aliasing, where possible? I've seen bugs in some gd libraries
-# that cause artefacts to appear when lines are anti-aliased. If your
-# image contains unexpected elements, turn aa off.
-anti_aliasing = yes
-
-# A parameter that must be set. Checks whether this file was imported.
-housekeeping = yes
+# Housekeeping parameters, which must be included
+# at the top level of the configuration.
+#
+# Don't adjust these, unless you know what you are doing, or
+# feel like experimenting
+
+anglestep       = 0.5
+minslicestep    = 10
+beziersamples   = 40 # bezier curves are drawn piece-wise
+                     # linear, with this many samples
+debug           = no
+warnings        = no
+imagemap        = no
+paranoid        = yes
+
+units_ok        = bupr
+units_nounit    = n
+
+# \t  tab
+# \s  any whitespace
+file_delim = \s
+# collapse adjacent whitespace
+# e.g. two spaces are treated as one, not as a missing field
+file_delim_collapse = yes
+
+# Record delimiter for parameter values that are lists, such as
+# hs1:0.25;hs2:0.10. By default, both ; and , are accepted
+#
+# e.g. hs1:0.25,hs2:0.10
+#      hs1:0.25;hs2:0.10
+list_record_delim = \s*[;,]\s*
+# Field delimiter specifies the assignment operator, e.g.
+list_field_delim  = \s*[:=]\s*]
+
+# Rule fields and other parameters accept var(VARIABLE) syntax
+# to reference parameters of data points. By default, if
+# VARIABLE does not exist, Circos quits with an error, unless
+# the skip parameter below is set.
+#
+# This feature is useful when you have data that don't always
+# have the same options. For example,
+#
+# chr1 10 20 a=10
+# chr1 50 60 b=10
+skip_missing_expression_vars = no
+
+# In old versions, data point parameters were referenced using _NAME_
+# syntax. This has been replaced with var(NAME). The _NAME_ syntax is
+# deprecated (for example, it will break when dealing with fields like
+# gene_a_1). If you must use it, set the parameter below.
+
+legacy_underline_expression_syntax = no
+
+# Magnification factor for text in SVG files.
+svg_font_scale = 1.3
+
+# default font - pick one of the keys from <fonts> block
+default_font   = default
+# default font name is used for SVG files for cases where
+# the font definition does not include a name
+# see etc/fonts.conf for details
+default_font_name  = Arial
+default_font_color = black
+
+# default color for cases when color is not specified
+default_color  = black
+
+<guides>
+thickness      = 1
+size           = 5
+type           = outline
+<object>
+all            = no
+ideogram       = no
+ideogram_label = no
+</object>
+<color>
+default = lblue
+text    = red
+</color>
+</guides>
+
+# Receive debug messages about actions
+#
+# Comma-separated list of one or more of the following
+#
+# summary   - top level indications of what's happening
+# chrfilter - ideogram filtering (parsing 'chromosomes' parameter)
+# conf      - configuration file
+# counter   - plot counters
+# spacing   - ideogram spacing
+# scale     - ideogram scaling
+# ideogram  - ideogram reporting
+# anglepos  - report angle positions for base pair coordinates
+# zoom      - zoom regions
+# layers    - specific plot z-layers
+# rules     - dynamic rules
+# text      - text tracks
+# heatmap   - detailed heatmap reports
+# brush     - brushes
+# color     - color allocation and definition
+# ticks     - tick marks and labels
+# timers    - some benchmark timings
+# cache     - caches
+# _all      - turn on all groups
+debug_group = summary
+
+# run length duration after which timing report is automatically
+# generated at the end of the run
+debug_auto_timer_report = 30
+
+debug_word_separator = " "
+debug_undef_text     = _undef_
+debug_empty_text     = _emptylist_
+
+# parameters passed to functions can be
+# validated to check consistency. turn this
+# off to speed things up
+debug_validate       = yes
+
+# Reformat numbers in debug output for consistency.
+# If you have a lot of debug output (e.g. -debug_group _all)
+# this will slow things considerably.
+debug_output_tidy    = no
+
+# pixel sub-sampling for text tracks
+text_pixel_subsampling = 1
+# array or span - use 'span' if applying snuggle refinement
+text_snuggle_method    = array
+
+# restrict names of parameters?
+# if 'yes' then only certain named parameters are allowed within
+# blocks and option fields for data
+#
+# if 'no' then you can define parameters with any name what-so-ever,
+# useful if you wish to define states or labels for your data
+#
+# e.g. hs1 10 20 0.5 paired=yes,special=no,myvar=0.5
+#
+# ordinarily, 'paired', 'special' and 'myvar' would not be allowed
+restrict_parameter_names = no
+
+# Unless set to 'yes', parameter names will be converted to lowercase
+case_sensitive_parameter_names = no
+
+# The location of configuration and data files will be guessed if
+# (a) configuration file is not specified
+# (b) data file paths are relative
+# Circos will look in the following locations, where
+# SCRIPTPATH is the location of the 'circos' script (e.g. /usr/local/bin) and
+# CWD is the current directory (where the 'circos' command was executed).
+# All paths under CWD will be scanned first, then under SCRIPTPATH.
+#
+# {CWD,SCRIPTPATH}/.
+# {CWD,SCRIPTPATH}/..
+# {CWD,SCRIPTPATH}/etc/
+# {CWD,SCRIPTPATH}/../etc
+# {CWD,SCRIPTPATH}/../../etc
+# {CWD,SCRIPTPATH}/data
+# {CWD,SCRIPTPATH}/../data
+# {CWD,SCRIPTPATH}/../../data
+#
+# If you would like to prepend this list with custom directories for
+# data files, enter them as a CSV list here
+# data_path = /home/martink/circos-tutorials
+# If the cache is static, it will always be used and will not be updated
+# unless it is deleted (use -color_cache_rebuild on the command line).
+# Otherwise, the cache will be updated if
+#  - config file is newer than cache file
+#  - list of colors in config file is different than in cache file
+color_cache_static = yes
+color_cache_file   = circos.colorlist
+color_lists_use    = yes
+# if the directory is not defined, then the system will guess a temporary
+# directory compatible with your operating system (using File::Temp)
+# color_cache_dir    = /tmp
+
+# Make some functions faster. This should always be 'yes' unless you
+# want things to run slowly or suspect deep issues.
+memoize = yes
+
+# This is a debugging flag and should be set to 'no' for regular use
+quit_on_dump = yes
+
+offsets = 0,0
+
+# Maximum number of image and data elements. If these are exceeded,
+# Circos will quit with an error. These values are arbitrary, but in
+# my experience images with significantly more data points than this
+# are uninterpretable.
+
+max_ticks            = 5000
+max_ideograms        = 200
+max_links            = 25000
+max_points_per_track = 25000
+
+# What to do when data is found for an ideogram that does not appear in the karyotype file.
+
+# Set to 'skip' or 'exit'
+undefined_ideogram = skip
+
+# Number of iterations for determining ideogram sizes when
+# relative scale is used.
+relative_scale_iterations = 10
+
+# min, max, average, mode             - based on scale statistics of ALL ideograms
+# minadj, maxadj, averageadj, modeadj - based on scale statistics of adjacent ideograms
+#
+# You can specify a fixed scale for spacing using a floating value
+#
+# e.g. relative_scale_spacing = 1.5
+relative_scale_spacing    = mode
+
+# What to do with out-of-range data. Either 'clip' or 'hide'
+data_out_of_range = clip
+
+# Track default directory
+track_defaults = etc/tracks
+
+# Use round brushes for elements with thickness greater than round_brush_min_thickness?
+round_brush_use           = yes
+round_brush_min_thickness = 5
+
+# Use anti aliasing, where possible? I've seen bugs in some gd libraries
+# that cause artefacts to appear when lines are anti-aliased. If your
+# image contains unexpected elements, turn aa off.
+anti_aliasing = yes
+
+# A parameter that must be set. Checks whether this file was imported.
+housekeeping = yes