result2 241111

cricos/circos-0.69-9/bin/circos

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+#!/usr/bin/env perl
+
+=pod
+
+=head1 NAME
+
+                                    ____ _
+                                   / ___(_)_ __ ___ ___  ___
+                                  | |   | | '__/ __/ _ \/ __|
+                                  | |___| | | | (_| (_) \__ \
+                                   \____|_|_|  \___\___/|___/
+
+                                                round is good
+
+circos - generate circular data visualizations
+
+=head1 SYNOPSIS
+
+  # without -conf Circos will search for configuration
+  circos
+
+  # use specific configuration file
+  circos -conf circos.conf 
+
+  # diagnose required modules
+  circos -modules
+
+  # detailed debugging for code components
+  # see http://www.circos.ca/documentation/tutorials/configuration/debugging
+  circos -debug_group GROUP1,[GROUP2,...]
+
+  # full debugging
+  circos -debug_group _all
+
+  # absolutely no reporting
+  circos ... [-silent]
+
+  # configuration dump of a block (or block tree) of
+  # any parameters that match REGEXP (optional)
+  circos -cdump [BLOCK1/[BLOCK2/...]]{:REGEXP}
+  circos -cdump ideogram
+  circos -cdump ideogram:label
+  circos -cdump ideogram/spacing
+
+  # override configuration parameters
+  circos -param image/radius=2000p -param ideogram/show=no
+
+  # for fun - randomize all colors in the image except for
+  # COLOR1, COLOR2,...
+  circos -randomcolor COLOR1,[COLOR2,...]
+  circos -randomcolor white,black
+
+  # brief help
+  circos -h
+
+  # man page
+  circos -man
+
+  # version
+  circos -v
+
+=head1 SUPPORT
+
+For support please use the Google Group
+
+L<https://groups.google.com/forum/#!forum/circos-data-visualization>
+
+=head1 DESCRIPTION
+
+Circos generates circular data visualizations. It is ideal for
+exploring relationships between objects or positions. 
+
+Circos does not have an interface. It is driven by plain-text configuration files (see below). This makes Circos scriptable and easily incorporated into automatic data analysis and reporting pipelines.
+
+=head2 Uses
+
+Circos was initially designed to visualize genomic information, specifically
+genomic rearrangements in tumor genomes. Although some important parameters in configuration files are named to be intuitve to biologists (e.g. "chromosomes"), Circos is not limited to the kind of data it can display. Circular heatmaps, histograms, scatter plots and other types of data displays can be easily made from data collected in other fields, such as meteorology, social science, and computer security.
+
+=head2 Salience and Relevance
+
+One of the challenges in creating data visualizations is to aptly map what is important (relevance) onto graphical elements that stand out from others (salience). Being able to emphasize (e.g. change color) or attenuate (e.g. add transparency or even hide) salience of information without changing the original data input files is a key feature of Circos.
+
+How data is displayed can be easily changed by writing rules, which are evaluated at run-time. Rules can be designed to apply to all data points or only to those that pass certain conditions. Conditions can be based on any property of the data (value, position, format). Rules can be chained into a decision tree making it possible to progressively change the format of data based on the output of other rules.
+
+=head2 Data Input Format
+
+Data input formats are plain-text and made to be as simple as possible. 
+
+=head2 Is it right for you?
+
+Circos is not a solution. It's a tool to solve visualization
+problems. For a given problem, you are not guaranteed that Circos is
+appropriate.
+
+=head1 CONFIGURATION
+
+Plain-text configuration file, which define a hierarchy of parameters, control creation of images. These files determine which files Circos uses for its input data, how the data are shown, the layout and formatting of elements in the image as well as system parameters that control low-level functions.
+
+=head2 Syntax
+
+Configuration is plain-text and composed of hierarchical blocks. Some
+blocks, such as C<<ideogram>> are mandatory, while others like
+C<<backgrounds>> are optional. 
+
+To get started, refer to the quick guide tutorial.
+
+L<http://www.circos.ca/documentation/tutorials/quick_guide>
+
+A typical configuration file might look like this
+ 
+  # chromosome name and length definitions
+  karyotype = myfile.txt
+
+  # image size and format 
+  <image>
+   ...
+  </image>
+ 
+  # position and size of ideograms
+  <ideogram>
+   ...
+  </ideogram>
+
+  # frequency, position and labeling of tick marks
+  <ticks>
+   ...
+  </ticks>
+
+  # position, type and format of data tracks
+  <plots>
+   <plot>
+     ...
+    # run-time rules to change data format and visibility
+     <rules>
+       <rule>
+        ...
+       </rule>
+       ...
+      </rules>
+   </plot>
+   ...
+  </plots>
+
+  # colors, fonts and fill patterns
+  <<include etc/colors_fonts_patterns.conf>>
+
+  # system parameters
+  <<include etc/housekeeping.conf>>
+
+=head2 Modularity
+
+Configuration from one file can be included in another, making it possible to have a very modular setup. For example, if several kinds of images are made for a single project, there can be project-wide configuration definitions which are then complemeted, and possibly overwritten, by image-specific configuration. 
+
+The C<<<include FILE>>> directive imports one configuration file into another.
+
+  # circos.conf
+  <<include ideogram.conf>>
+
+  # ideogram.conf
+  <<include ideogram.label.conf>>
+  <<include ideogram.size.conf>>
+  ...
+
+In the tutorials, you'll find that the C<<ideogram>> and C<<ticks>> blocks are imported into the main configuration file. Because these blocks can get quite large, the main configuration file is more legible if they are relegated to separate files.
+
+Parameter definitions that do not frequently change, such as color and font definitions, are conventionally imported from files found in F<etc/> in the distribution. Every Circos image should have
+
+  # image size, output file name
+  <image>
+  <<include etc/image.conf>>
+  </image>
+  # color names and lists, location of fonts, fill patterns
+  <<include etc/colors_fonts_patterns.conf>>
+  # low-level system parameters
+  <<include etc/housekeeping.conf>>
+
+=head2 Overriding with *
+
+To override a parameter that has been included from a file, use the C<*> suffix. The suffix is required because multiple definitions of a parameter are not allowed, except in cases where a parameter is may have more than one value.
+
+  <image>
+  # included file defines 'radius'
+  <<include etc/image.conf>>
+  # this will override the radius value
+  radius* = 2500p
+  </image>
+
+The C<*> suffix can be repeated to specify which value takes precedence in a block.
+
+  radius   = 1500p
+  radius*  = 2500p
+  radius** = 3000p # this instance of radius will be used
+
+=head2 Overriding with Command Line
+
+Any configuration parameter in a unique block name can be specified on
+the command line using
+
+  -param PATH/PARAM=value
+
+For example,
+
+  <ideogram>
+    show = no
+    ...
+  </ideogram>
+  
+  -param ideogram/show=no
+
+and
+
+  <ideogram>
+    <spacing>
+      default = 0.01r
+    </spacing>
+    ...
+  </ideogram>
+  
+  -param ideogram/spacing/default=0.01r
+
+=head2 Accessing Parameters 
+
+The C<conf()> function is used in the configuration file to retrieve the value of a parmameter. It can be used to retrieve any parameter, not just those set by C<-param>). This provides a very flexible system for changing the configuration at the command line.
+
+For example, in this case the karyotype file name will change as the C<species> parameter is changed either in the configuration file or using the <C-param> flag. Similarly, the color palette size and name can be adjusted.
+
+  # circos.conf
+  species    = human
+  palette    = blues
+  num_colors = 9
+  karytotype = data/karyotype/karyotype.conf(species).txt
+  ...
+  <plots>
+   color     = conf(palette)-seq-conf(num_colors)
+   ...
+
+  > circos ... -param species=rat -param palette=reds -param num_colors=5
+   
+Multiple parameters can be redefined, each with its own C<-param> flag
+
+  -param show_ticks=no -param image/radius=2000p
+
+=head2 Merging Blocks
+
+Multiple instances of the following blocks are automatically merged: C<<ideogram>>, C<<colors>>, C<<fonts>>, C<<paterns>>, C<<image>>, C<<links>>, C<<plots>> and C<<highlights>>.
+
+The purpose of this is to allow you to add to canonical definitions.
+
+  # this file defines default <colors>, <fonts> and <patterns>
+  <<include etc/colors_fonts_patterns.conf>>
+
+  # add to the colors block
+  <colors>
+  mycolor = 150,25,25
+  </colors>
+
+=head2 Absolute and Relative Paths
+
+The use of absolute paths are used in configuration file is discouraged. Doing so makes your configuration less modular and unuseable on another system.
+
+For example, if Joe's files are organized thus
+
+  /user/joe/project/
+                    data/genes.txt
+                    etc/circos.conf
+
+he could use
+
+  file = /user/joe/project/data/genes.txt
+
+and run Circos from his home directory
+
+  > cd ~
+  > circos -conf project/etc/circos.conf
+
+It would be much better for him to define
+
+  file = data/genes.txt
+
+and run Circos from the project/ directory
+
+  > cd ~/project
+  > circos
+
+Now, if he creates a tarball of all the project files (e.g. C<project.tgz>), anyone could use the files by executing exactly the same commands.
+
+When you define a file with a relative path, such as
+
+  file = data/genes.txt
+
+Circos will look for this file relative to several reasonable start points, such as the location of the configuration file that you are using, one level up from the configuration location, your current directory, and so on.
+
+To see where Circos is searching for files, use
+  
+  > circos -debug_group io
+
+This is the same mechanism used to find the initial configuration file. If you run Circos without the C<-conf> flag,
+
+  > cd ~/project
+  > circos
+
+then Circos will look for
+
+  ~/project/circos.conf
+  ~/project/etc/circos.conf
+  ~/project/data/circos.conf
+  ~/project/../circos.conf
+  ~/project/../etc/circos.conf
+  ...
+
+If the configuration file cannot be found, Circos will default to looking into its distribution directory.
+
+Users who are unaware of this feature often manage to get away with unorganized project files because this automatic file search feature. The purpose of this feature is to make your life easier when you know what you're doing -- not necessarily to make it possible when you don't know what you're doing. 
+
+If you want to redefine the search paths, see the C<data_path> parameter in C<etc/housekeeping.conf> in the distribution directory, or overide it in your configuration file
+
+  <<include etc/housekeeping.conf>>
+  data_path* = ...
+
+=head1 OPTIONS
+
+=head2 Configuration
+
+=over
+
+=item -configfile FILE
+
+Name of configuration file. This is required.
+
+Circos will attempt to guess the location of this file, searching for
+C<circos.conf> in C<.>, C<..>, and C<../..>. This is described above.
+
+=back
+
+=head2 Output Format
+
+=over
+
+=item -png, -nopng
+
+=item -svg, -nosvg
+
+Toggles output of PNG and SVG files.
+
+=back
+
+=head2 Image Elements
+
+=over
+
+=item -show_ticks, -noshow_ticks
+
+=item -show_tick_labels, -noshow_tick_labels
+
+Override the display of ticks and their labels. These are both usually defined in the <ticks> block.
+
+These flags are shortcuts to
+
+  -param show_ticks=no
+  -param show_tick_labels=no
+
+=back
+
+=head2 Output Paths
+
+=over 
+
+=item -outputdir DIR, -dir DIR
+
+=item -outputfile FILE, -file FILE
+
+Change the output directory and filename. The FILE can contain a path.
+
+=back 
+
+=head2 Debugging
+
+=over
+
+=item -debug 
+
+Turn on basic debugging output. Reports information from 
+
+  image, io, layer, summary, timer
+
+debug groups (see below).
+
+=item -debug_group {+-}GROUP1,[{+-}GROUP2,...]
+
+Turn on debugging output for specific groups. For a list of groups, see
+
+L<http://www.circos.ca/documentation/tutorials/configuration/debugging>
+
+To add a group to the output prefix it with +. To remove it, with -.
+
+  # use default debugging groups but exclude layer and io
+  -debug -debug_group -layer,-io
+
+  # use default debugging groups and add spacing
+  -debug -debug_group +spacing
+
+  # explicitly specify the groups
+  -debug_group png,io,timer
+
+To list the groups that are supported, use the flag without an argument
+
+  -debug_group
+
+Those listed with a "*" are turned on by default. To change this, adjust C<debug_group> in C<etc/housekeeping.conf> in the distribution directory.
+
+=item -time
+
+Report timing information. Same as C<-debug_group +timer>.
+
+=item -silent 
+
+Generate no reporting.
+
+=item -paranoid, -noparanoid
+
+Run in paranoid mode (default), or not. The default for this setting is defined by C<paranoid> in C<etc/housekeeping.conf>.
+
+=item -warnings, -nowarnings
+
+Display warnings, or not (default). The default for this setting is defined by C<warnings> in C<etc/housekeeping.conf>.
+
+=item -fakeerror
+=item -fakeerror CAT
+=item -fakeerror ,ID
+=item -fakeerror CAT,ID
+
+Fake an error by displaying the error message for category CAT and error name ID. If one or neither are specified, lists which errors are available. 
+
+Unless you truly enjoy seeing error messages, there should be little reason for you to want to use this.
+
+=back
+
+=head2 Usage
+
+=over
+
+=item -version
+
+Show the version.
+
+=item -help
+
+Show brief usage synopsis.
+
+=item -man
+
+Show man page.
+
+=back
+
+=head2 Goofing Around
+
+=over
+
+=item -randomcolor [color1,color2,...]
+
+Randomize the color of every element in the image, except for an optional list of colors.
+
+For example, to keep the background white and anything that is black,
+
+  -randomcolor white,black
+
+=back
+
+=head1 DOCUMENTATION
+
+For full documentation, see
+
+L<http://www.circos.ca/documentation/tutorials>
+
+=back
+
+=cut
+
+use strict;
+use warnings;
+use FindBin;
+use Getopt::Long qw(:config pass_through posix_default auto_abbrev);
+use Pod::Usage;
+
+use lib "$FindBin::RealBin";
+use lib "$FindBin::RealBin/../lib";
+use lib "$FindBin::RealBin/lib";
+use Circos;
+
+use Cwd;
+use Circos::Debug;
+use Circos::Error;
+
+our %OPT = (_argv=>join(" ",@ARGV),_cwd=>cwd());
+
+my $option_success = GetOptions(\%OPT,
+
+																'configfile=s',
+																'param=s@',
+																'cdump:s',
+
+																'dir=s',
+																'file=s',
+																'outputdir=s',
+																'outputfile=s',
+																'png!',
+																'svg!',
+																'imagemap',
+
+																'color_cache_rebuild',
+																'color_cache_static',
+																'randomcolor:s',
+																'wmmn:s',
+
+																'help',
+																'man',
+																'silent',
+																'paranoid!',
+																'warnings!',
+																'fakeerror:s',
+																'debug+',
+																'debug_group:s',
+																'version',
+																'time',
+																'timer',
+																'timers',
+
+																'show_ticks!',
+																'show_tick_labels!',
+														);
+fatal_error("configuration","bad_command_line_options",join(" ",@ARGV)) if ! $option_success || @ARGV;
+pod2usage()            if $OPT{'help'};
+pod2usage(-verbose=>2) if $OPT{'man'};
+Circos->run(%OPT);
+
+# -------------------------------------------------------------------
+
+=pod
+
+=head1 AUTHOR
+
+Martin Krzywinski 
+L<martink@bcgsc.ca> 
+L<http://mkweb.bcgsc.ca> 
+L<@MKrzywinski>
+
+Canada's Michael Smith Genome Sciences Centre
+100-570 W 7th Ave
+Vancouver BC V5Z 4S6 Canada
+
+L<http://www.bcgsc.ca>
+
+=head1 RESOURCES
+
+L<http://www.circos.ca>
+
+L<https://groups.google.com/forum/#!forum/circos-data-visualization>
+
+=head1 CITING
+
+If you are using Circos in a publication, please cite as
+
+Krzywinski, M., J. Schein, I. Birol, J. Connors, R. Gascoyne,
+D. Horsman, S. Jones, and M. Marra. 2009. Circos: an Information
+Aesthetic for Comparative Genomics. Genome Res 19:1639-1645.
+
+=head1 CONTRIBUTORS
+
+Ken Youens-Clark L<kyclark@gmail.com>
+
+=head1 SEE ALSO
+
+Hive plots L<http://www.hiveplot.com>
+
+=head1 COPYRIGHT & LICENSE
+
+Copyright 2004-2017 Martin Krzywinski, all rights reserved.
+
+This script is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This script is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this script; if not, write to the Free Software Foundation,
+Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+=cut

cricos/circos-0.69-9/bin/circos.conf

@@ -0,0 +1,270 @@
+karyotype = data/data.txt # copy.txt
+
+<ideogram> 
+<spacing>
+#default : the space distance between nodes
+default=0.0035r
+#default=1u 
+</spacing>
+
+radius                  = 0.75r     # big circle (=b.c)
+thickness               = 50p       # thick of b.c
+fill                    = yes       # filled in b.c
+stroke_color            = dgrey     # color of b.c
+stroke_thickness        = 1p        # b.c's box's boundary thickness 
+
+#BANDS
+show_bands              = yes
+fill_bands              = yes
+band_stroke_thickness   = 20
+band_stroke_color       = white
+band_transparency       = 2
+
+#LABELS
+show_label      = yes
+# see etc/fonts.conf for list of font names
+#label_radius   = (dims(ideogram,radius_inner) + dims(ideogram,radius_outer))/2
+label_font      = bold
+#label_center    = yes
+label_size      = 23
+label_radius    = 1r+40p #+50p
+label_with_tag  = yes
+label_case      = upper
+label_parallel  = no
+</ideogram>
+
+show_ticks       = yes
+show_tick_labels = yes
+show_grid        = yes
+
+<ticks>
+grid_start     = 0.5r
+grid_end       = 0.975r
+grid_color     = black
+grid_thickness = 1p
+
+skip_first_label  = no
+skip_last_label   = no
+radius            = dims(ideogram,radius_outer)
+tick_separaation  = 30p
+label_separation  = 30p
+multiplier        = 0.01    #current pin multipy with tag ex. if want 1-14 but (100 ~1400) use this.
+color             = black
+thickness         = 3p
+size              = 10p
+
+<tick>      # b.c's upper black line length     # if too much big size, no show label units
+spacing     = 100u
+show_label  = yes
+label_size  = 15p
+thickness   = 3p
+color       = black
+</tick>
+
+<tick>      # b.c's upper red line length    
+spacing     = 100u
+show_label  = yes
+label_size  = 12p
+thickness   = 1p
+color       = red
+format      = %d
+</tick>
+
+# ------ original ----------
+# ------ Customized --------
+<tick>                      # where? band orange line
+spacing              = 99.9u
+grid_start           = 0.80r
+grid_end             = 0.99r
+grid_color           = orange
+grid_thickness       = 2p
+grid                 = yes
+</tick>
+
+<tick>                      # where? band orange line
+spacing              = 99.9u
+grid_start           = 0.48r
+grid_end             = 0.49r
+grid_color           = orange
+grid_thickness       = 2p
+grid                 = yes
+</tick>
+
+<tick>                          # 중간 pass
+radius               = 0.79r
+spacing              = 99.9u
+size                 = 3p
+thickness            = 3p
+show_label           = yes
+label_size           = 10p
+label_with_tag       = yes
+format               = %d
+</tick>
+
+<tick>                           # Link용 pass
+radius               = 0.5 #0.48r
+spacing              = 0.99u
+size                 = 1p
+thickness            = 2p
+show_label           = yes
+label_size           = 10p
+label_multiplier     = 0.01
+orientation          = out
+format               = %d
+</tick>
+
+# <tick>
+# spacing        = 100u
+# thickness      = 3p
+# color          = green
+# grid           = yes
+# grid_color     = red
+# grid_thickness = 3p
+# grid_start     = 0.3r
+# grid_end       = 0.8r
+# </tick>
+
+# <tick>
+# spacing        = 1u
+# color          = blue
+# grid           = yes
+# grid_color     = blue
+# grid_thickness = 1p
+# grid_start     = 0.55r
+# grid_end       = 0.95r
+# </tick>
+# ------ Customized --------
+</ticks>
+
+
+##################### BAND LABEL
+<plots>
+<plot>
+type            = text
+color           = black
+file            = data/band.txt
+r0              = 0.83r
+r1              = 1r
+label_size      = 18p
+label_font      = italicbold
+label_parallel  = no
+#label_rotated  = yes
+
+# label_snuggle        = yes
+# max_snuggle_distance = 1r
+# snuggle_tolerance    = 0.25r
+# snuggle_sampling     = 2
+# snuggle_refine       = yes
+</plot>
+
+# <plot>
+# type = histogram
+# file = data/hist.txt
+# r0 = 0.65r
+# r1 = 0.78r
+# fill_color = dgrey
+# thickness = 2p
+# min=0
+# max=200
+# extend_bin  = no
+# <rules>
+# <rule>
+# condition  = var(value) > 100
+# fill_color = vdblue
+# </rule>
+# </rules>
+# <backgrounds>
+# <background>
+# color = vvlgrey
+# </background>
+# </backgrounds>
+# </plot>
+
+# <plot>
+# type = heatmap
+# r1 = 0.64r
+# r0 = 0.59r
+# file = data/hist.txt
+# color  = spectral-6-div
+# color_alt = black,spectral-5-div,grey
+# scale_log_base = 1.0
+# stroke_thickness = undef
+# min = 0
+# max = 200
+# # minsize = 1u
+# # thickness = 20
+# # margin = 1u
+# </plot>
+
+# <plot>
+# type = tile
+# r1 = 0.58r
+# r0 = 0.5r
+# file = data/hist.txt
+# orientation = out
+# layers = 5
+# layer_overflow = grow
+# layer_overflow_color = red
+# thickness = 15
+# padding = 10
+# stroke_thickness = undef
+# stroke_color     = dgreen
+# color            = dgreen
+# <backgrounds>
+# <background>
+# y0 = 0.80r
+# color = grey_a1
+# </background>
+# <background>
+# y0 = 0.60r
+# y1 = 0.80r
+# color = grey_a2
+# </background>
+# <background>
+# y0 = 0.40r
+# y1 = 0.60r
+# color = grey_a3
+# </background>
+# <background>
+# y0 = 0.20r
+# y1 = 0.40r
+# color = grey_a4
+# </background>
+# <background>
+# y1 = 0.20r
+# color = grey_a5
+# </background>
+# </backgrounds>
+# <rules>
+# <rule>
+# condition  = var(size) > 100
+# color      = pred
+# </rule>
+# </rules>
+# scale_log_base = 0.25
+# minsize = 1u
+# margin = 1u
+# </plot>
+</plots>
+###################### LINKS
+# <links>
+# <link>
+# file            = data/link.txt
+# radius          = 0.7r #0.7r
+# bezier_radius   = 0.05r #0.05r #0.05r
+# bezier_radius_purity = 0.5 #0.5
+# thickness       = 10p
+# ribbon          = no #wider
+# </link>
+# </links>
+
+<image>
+#include from circos distribution
+angle_offset* = 20
+<<include etc/image.conf>>
+#to modify the size of the output image, default is 1500
+#radius* = 100p
+</image>
+
+<<include etc/colors_fonts_patterns.conf>>
+<<include etc/housekeeping.conf>>

cricos/circos-0.69-9/bin/circos.exe

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a0a9e2a71cf68809369ff7366b2aca8e69a38091bc5d9285b27a21931948c93b
+size 5401162

cricos/circos-0.69-9/bin/compile.bat

@@ -0,0 +1 @@
+pp -M Carp -M Clone -M Config::General -M Cwd -M Data::Dumper -M Digest::MD5 -M File::Basename -M File::Spec::Functions -M File::Temp -M FindBin -M Font::TTF:: -M GD -M GD::Polyline -M Getopt::Long -M IO::File -M List::MoreUtils -M List::Util -M Math::Bezier -M Math::BigFloat -M Math::Round -M Math::VecStat -M Memoize -M POSIX -M Params::Validate -M Pod::Usage -M Readonly -M Regexp::Common -M SVG -M Set::IntSpan -M Statistics::Basic -M Storable -M Sys::Hostname -M Text::Balanced -M Text::Format -M Time::HiRes  -l c:\Dwimperl\c\bin\libgd-2_.dll -l c:\Dwimperl\c\bin\libfreetype-6_.dll -l c:\Dwimperl\c\bin\libpng12-0_.dll -l c:\Dwimperl\c\bin\libpng15-15_.dll -l c:\Dwimperl\c\bin\libXpm_.dll -l c:\Dwimperl\c\bin\libz_.dll -l c:\Dwimperl\c\bin\libiconv-2_.dll -l c:\Dwimperl\c\bin\libjpeg-62_.dll -o circos.exe circos

cricos/circos-0.69-9/bin/compile.make

@@ -0,0 +1,8 @@
+#!/bin/bash
+#
+# create batch file to compile Circos for Windows systems
+#
+
+LIBDIR="c:\\\Dwimperl\\\c\\\bin"
+LINK="-l $LIBDIR\\\libgd-2_.dll -l $LIBDIR\\\libfreetype-6_.dll -l $LIBDIR\\\libpng12-0_.dll -l $LIBDIR\\\libpng15-15_.dll -l $LIBDIR\\\libXpm_.dll -l $LIBDIR\\\libz_.dll -l $LIBDIR\\\libiconv-2_.dll -l $LIBDIR\\\libjpeg-62_.dll" 
+./circos -modules | shrinkwrap | c2 | sed 's/^/-M /g' | unsplit -delim " " | sed 's/::Font/::/' | awk -v LINK="$LINK" '{print "pp "$0,LINK" -o circos.exe circos"}'

cricos/circos-0.69-9/bin/data/band.txt

@@ -0,0 +1,79 @@
+var21  0     100    Kappa1       
+var21  101   200    Kappa2       
+var21  201   300    Kappa3       
+var22  0     100    Chi0         
+var22  100   200    Chi0n        
+var22  201   300    Chi0v        
+var22  301   400    Chi1         
+var22  401   500    Chi1n        
+var22  501   600    Chi1v        
+var22  601   700    Chi2n        
+var22  701   800    Chi2v        
+var22  801   900    Chi3n        
+var22  901   1000   Chi3v        
+var22  1001  1100   Chi4n         
+var22  1101  1200   Chi4v         
+var22  1201  1300   ChiNn_        
+var22  1301  1400   ChiNv_        
+var29  0     100    PEOE_VSA1     
+var29  101   200    PEOE_VSA2     
+var29  201   300    PEOE_VSA3     
+var29  301   400    PEOE_VSA4     
+var29  401   500    PEOE_VSA5     
+var29  501   600    PEOE_VSA6     
+var29  601   700    PEOE_VSA7     
+var29  701   800    PEOE_VSA8     
+var29  801   900    PEOE_VSA9     
+var29  901   1000   PEOE_VSA10    
+var29  1001  1100   PEOE_VSA11    
+var29  1101  1200   PEOE_VSA12    
+var29  1201  1300   PEOE_VSA13    
+var29  1301  1400   PEOE_VSA14    
+var30  0     100    SMR_VSA1      
+var30  101   200    SMR_VSA2      
+var30  201   300    SMR_VSA3      
+var30  301   400    SMR_VSA4      
+var30  401   500    SMR_VSA5      
+var30  501   600    SMR_VSA6      
+var30  601   700    SMR_VSA7      
+var30  701   800    SMR_VSA8      
+var30  801   900    SMR_VSA9      
+var30  901   1000   SMR_VSA10     
+var31  0     100    SlogP_VSA1    
+var31  101   200    SlogP_VSA2    
+var31  201   300    SlogP_VSA3    
+var31  301   400    SlogP_VSA4    
+var31  401   500    SlogP_VSA5    
+var31  501   600    SlogP_VSA6    
+var31  601   700    SlogP_VSA7    
+var31  701   800    SlogP_VSA8    
+var31  801   900    SlogP_VSA9    
+var31  901   1000   SlogP_VSA10   
+var31  1001  1100   SlogP_VSA11   
+var31  1101  1200   SlogP_VSA12   
+var32  0     100    EState_VSA1   
+var32  101   200    EState_VSA2   
+var32  201   300    EState_VSA3   
+var32  301   400    EState_VSA4   
+var32  401   500    EState_VSA5   
+var32  501   600    EState_VSA6   
+var32  601   700    EState_VSA7   
+var32  701   800    EState_VSA8   
+var32  801   900    EState_VSA9   
+var32  901   1000   EState_VSA10  
+var32  1001  1100   EState_VSA11  
+var33  0     100    VSA_EState1   
+var33  101   200    VSA_EState2   
+var33  201   300    VSA_EState3   
+var33  301   400    VSA_EState4   
+var33  401   500    VSA_EState5   
+var33  501   600    VSA_EState6   
+var33  601   700    VSA_EState7   
+var33  701   800    VSA_EState8   
+var33  801   900    VSA_EState9   
+var33  901   1000   VSA_EState10  
+var37  0     100    PMI1          
+var37  101   200    PMI2          
+var37  201   300    PMI3          
+var38  0     100    NPR1          
+var38  101   200    NPR2          

cricos/circos-0.69-9/bin/data/data copy.txt

@@ -0,0 +1,49 @@
+chr - var1   Mol_Weight          0 1   lpred
+chr - var2   Mol_MR              0 1   lpred
+chr - var3   Mol_TPSA            0 1   lpred
+chr - var4   Mol_logP            0 1   lpred
+chr - var5   RotatedBonds        0 1   lppurple
+chr - var6   HeavyAtom           0 1   lppurple
+chr - var7   numHAcceptor        0 1   lppurple
+chr - var8   numHDoner           0 1   lppurple
+chr - var9   numHeteroatom       0 1   lppurple
+chr - var10  numValenceElec      0 1   lppurple
+chr - var11  NHOHCount           0 1   lpblue
+chr - var12  NOCount             0 1   lpblue
+chr - var13  RingCount           0 1   lppurple
+chr - var14  numAromaticR        0 1   lppurple
+chr - var15  numSaturateR        0 1   lppurple
+chr - var16  numAliphaticR       0 1   lppurple
+chr - var17  LabuteASA           0 1   lppurple
+chr - var18  BalabanJs           0 1   lppurple
+chr - var19  BertzCTs            0 1   lppurple
+chr - var20  Ipc                 0 1   lppurple
+chr - var21  Kappa_Series        0 3   pgreen
+chr - var22  Chi_Series          0 14  pgreen
+chr - var23  Phi                 0 1   lppurple
+chr - var24  HallKierAlpha       0 1   lppurple
+chr - var25  NumAmideBonds       0 1   lppurple
+chr - var26  FractionCSP3        0 1   lppurple
+chr - var27  NumSpiroAtoms       0 1   lppurple
+chr - var28  NumBridgeheadAtoms  0 1   lppurple
+chr - var29  PEOE_VSA_Series     0 14  pgreen
+chr - var30  SMR_VSA_Series      0 10  pgreen
+chr - var31  SlogP_VSA_Series    0 12  pgreen
+chr - var32  EState_VSA_Series   0 11  pgreen
+chr - var33  VSA_EState_Series   0 10  pgreen
+chr - var34  Asphericity         0 1   lppurple
+chr - var35  PBF                 0 1   lppurple
+chr - var36  PMI_Series          0 3   lppurple
+chr - var37  NPR_Series          0 2   lppurple
+chr - var38  RadiusOfGyration    0 1   lppurple
+chr - var39  InertialShapeFactor 0 1   lppurple
+chr - var40  Eccentricit         0 1   lppurple
+chr - var41  SpherocityIndex     0 1   lppurple
+chr - var42  MQNs                0 1   vlporange
+chr - var43  AUTOCORR2D          0 1   vlporange
+chr - var44  BCUT2D              0 1   vlporange
+chr - var45  AUTOCORR3D          0 1   vlporange
+chr - var46  RDF                 0 1   vlporange
+chr - var47  MORSE               0 1   vlporange
+chr - var48  WHIM                0 1   vlporange
+chr - var49  GETAWAY             0 1   vlporange

cricos/circos-0.69-9/bin/data/data.txt

@@ -0,0 +1,49 @@
+chr - var1   MolWT          0 100   lpred
+chr - var2   MolMR              0 100   lpred
+chr - var3   MolTPSA            0 100   lpred
+chr - var4   MolLogP            0 100   lpred
+chr - var5   RotatedBonds        0 100   lpred
+chr - var6   HeavyAtom           0 100   lpred
+chr - var7   numHAcceptor        0 100   lpred
+chr - var8   numHDoner           0 100   lpred
+chr - var9   numHeteroatom       0 100   lpred
+chr - var10  numValenceElec      0 100   lpred
+chr - var11  NHOHCount           0 100   lpred
+chr - var12  NOCount             0 100   lpred
+chr - var13  RingCount           0 100   lpred
+chr - var14  numAromaticR        0 100   lpred
+chr - var15  numSaturateR        0 100   lpred
+chr - var16  numAliphaticR       0 100   lpred
+chr - var17  LabuteASA           0 100   lpred
+chr - var18  BalabanJs           0 100   lpred
+chr - var19  BertzCTs            0 100   lpred
+chr - var20  Ipc                 0 100   lpred
+chr - var21  Kappa_Series        0 300   lpred
+chr - var22  Chi_Series          0 1400  lpred
+chr - var23  Phi                 0 100   lpred
+chr - var24  HallKierAlpha       0 100   lpred
+chr - var25  NumAmideBonds       0 100   lpred
+chr - var26  FractionCSP3        0 100   lpred
+chr - var27  NumSpiroAtoms       0 100   lpred
+chr - var28  NumBridgeheadAtoms  0 100   lpred
+chr - var29  PEOE_VSA_Series     0 1400  lpred
+chr - var30  SMR_VSA_Series      0 1000  lpred
+chr - var31  SlogP_VSA_Series    0 1200  lpred
+chr - var32  EState_VSA_Series   0 1100  lpred
+chr - var33  VSA_EState_Series   0 1000  lpred
+chr - var34  AUTOCORR2D          0 100   lpred
+chr - var35  BCUT2D              0 100   lpred
+chr - var36  PBF                 0 100   lpblue
+chr - var37  PMI_Series          0 300   lpblue
+chr - var38  NPR_Series          0 200   lpblue
+chr - var39  RadiusOfGyration    0 100   lpblue
+chr - var40  InertialShapeFactor 0 100   lpblue
+chr - var41  Eccentricit         0 100   lpblue
+chr - var42  Asphericity         0 100   lpblue
+chr - var43  SpherocityIndex     0 100   lpblue
+chr - var44  MQNs                0 100   lpblue
+chr - var45  AUTOCORR3D          0 100   lpblue
+chr - var46  RDF                 0 100   lpblue
+chr - var47  MORSE               0 100   lpblue
+chr - var48  WHIM                0 100   lpblue
+chr - var49  GETAWAY             0 100   lpblue

cricos/circos-0.69-9/bin/data/data2.txt

@@ -0,0 +1,49 @@
+chr - var1   Mol_Weight          0 100   
+chr - var2   Mol_MR              0 100   
+chr - var3   Mol_TPSA            0 100   
+chr - var4   Mol_logP            0 100   
+chr - var5   RotatedBonds        0 100   
+chr - var6   HeavyAtom           0 100   
+chr - var7   numHAcceptor        0 100   
+chr - var8   numHDoner           0 100   
+chr - var9   numHeteroatom       0 100   
+chr - var10  numValenceElec      0 100   
+chr - var11  NHOHCount           0 100   
+chr - var12  NOCount             0 100   
+chr - var13  RingCount           0 100   
+chr - var14  numAromaticR        0 100   
+chr - var15  numSaturateR        0 100   
+chr - var16  numAliphaticR       0 100   
+chr - var17  LabuteASA           0 100   
+chr - var18  BalabanJs           0 100   
+chr - var19  BertzCTs            0 100   
+chr - var20  Ipc                 0 100   
+chr - var21  Kappa_Series        0 300   
+chr - var22  Chi_Series          0 1400  
+chr - var23  Phi                 0 100   
+chr - var24  HallKierAlpha       0 100   
+chr - var25  NumAmideBonds       0 100   
+chr - var26  FractionCSP3        0 100   
+chr - var27  NumSpiroAtoms       0 100   
+chr - var28  NumBridgeheadAtoms  0 100   
+chr - var29  PEOE_VSA_Series     0 1400  
+chr - var30  SMR_VSA_Series      0 1000  
+chr - var31  SlogP_VSA_Series    0 1200  
+chr - var32  EState_VSA_Series   0 1100  
+chr - var33  VSA_EState_Series   0 1000  
+chr - var34  Asphericity         0 100   
+chr - var35  PBF                 0 100   
+chr - var36  PMI_Series          0 300   
+chr - var37  NPR_Series          0 200   
+chr - var38  RadiusOfGyration    0 100   
+chr - var39  InertialShapeFactor 0 100   
+chr - var40  Eccentricit         0 100   
+chr - var41  SpherocityIndex     0 100   
+chr - var42  MQNs                0 100   
+chr - var43  AUTOCORR2D          0 100   
+chr - var44  BCUT2D              0 100   
+chr - var45  AUTOCORR3D          0 100   
+chr - var46  RDF                 0 100   
+chr - var47  MORSE               0 100   
+chr - var48  WHIM                0 100   
+chr - var49  GETAWAY             0 100   

cricos/circos-0.69-9/bin/data/hist copy 2.txt

@@ -0,0 +1,63 @@
+hs1   0   1      529.0000 
+hs2   1   2      0.0000   
+hs3   3   4      0.0000   
+hs4   5   6      0.0000   
+hs5   7   8      1.0000   
+hs6   9   10     0.0000   
+hs7   11  12     0.0000   
+hs8   13  14     0.0000   
+hs9   15  16     0.0000   
+hs10  17  18     1.0000   
+hs11  19  20     0.0000   
+hs12  21  22     0.0000   
+hs13  23  24     0.0000   
+hs14  25  26     0.0000   
+hs15  27  28     1.0000   
+hs16  29  30     0.0000   
+hs17  31  32     0.0000   
+hs18  33  34     0.0000   
+hs19  35  36     0.0000   
+hs20  37  38     1.0000   
+hs21  39  41     0.0000   
+hs22  42  55     0.0000   
+hs23  56  57     0.0000   
+hs24  58  59     0.0000   
+hs25  60  61     1.0000   
+hs26  62  63     0.0000   
+hs27  64  65     0.0000   
+hs28  66  67     0.0000   
+hs29  68  82     0.0000   
+hs30  83  92     1.0000   
+hs31  93  104    0.0000   
+hs32  105 115    0.0000   
+hs33  116 125    0.0000   
+hs34  126 127    0.0000   
+hs35  128 129    1.0000   
+hs36  130 133    0.0000   
+hs37  134 135    0.0000   
+hs38  136 137    0.0000   
+hs39  138 139    0.0000   
+hs40  140 140    1.0000   
+hs41  146 147    0.0000   
+hs42  148 149    0.0000   
+hs43  150 151    0.0000   
+hs44  152 153    0.0000   
+hs45  154 155    1.0000   
+hs46  156 157    0.0000   
+hs47  158 160    0.0000   
+hs48  160 161    0.0000   
+hs49  162 163    1.0000   
+
+-9.66930e+01,  3.98700e+11,  7.97400e+11,  1.19610e+12,
+        1.59480e+12,  1.99350e+12,  2.39220e+12,  2.79090e+12,
+        3.18960e+12,  3.58830e+12,  3.98700e+12,  4.38570e+12,
+        4.78440e+12,  5.18310e+12,  5.58180e+12,  5.98050e+12,
+        6.37920e+12,  6.77790e+12,  7.17660e+12,  7.57530e+12,
+        7.97400e+12,  8.37270e+12,  8.77140e+12,  9.17010e+12,
+        9.56880e+12,  9.96750e+12,  1.03662e+13,  1.07649e+13,
+        1.11636e+13,  1.15623e+13,  1.19610e+13,  1.23597e+13,
+        1.27584e+13,  1.31571e+13,  1.35558e+13,  1.39545e+13,
+        1.43532e+13,  1.47519e+13,  1.51506e+13,  1.55493e+13,
+        1.59480e+13,  1.63467e+13,  1.67454e+13,  1.71441e+13,
+        1.75428e+13,  1.79415e+13,  1.83402e+13,  1.87389e+13,
+        1.91376e+13,  1.95363e+13

cricos/circos-0.69-9/bin/data/hist copy 3.txt

@@ -0,0 +1,49 @@
+hs1   0   1      529.0000  
+hs2   1   2      0.0000    
+hs3   3   4      0.0000    
+hs4   5   6      0.0000    
+hs5   7   8      1.0000    
+hs6   9   10     0.0000    
+hs7   11  12     0.0000    
+hs8   13  14     0.0000    
+hs9   15  16     0.0000    
+hs10  17  18     1.0000    
+hs11  19  20     0.0000    
+hs12  21  22     0.0000    
+hs13  23  24     0.0000    
+hs14  25  26     0.0000    
+hs15  27  28     1.0000    
+hs16  29  30     0.0000    
+hs17  31  32     0.0000    
+hs18  33  34     0.0000    
+hs19  35  36     0.0000    
+hs20  37  38     1.0000    
+hs21  39  41     0.0000    
+hs22  42  55     0.0000    
+hs23  56  57     0.0000    
+hs24  58  59     0.0000    
+hs25  60  61     1.0000    
+hs26  62  63     0.0000    
+hs27  64  65     0.0000    
+hs28  66  67     0.0000    
+hs29  68  82     0.0000    
+hs30  83  92     1.0000    
+hs31  93  104    0.0000    
+hs32  105 115    0.0000    
+hs33  116 125    0.0000    
+hs34  126 127    0.0000    
+hs35  128 129    1.0000    
+hs36  130 133    0.0000    
+hs37  134 135    0.0000    
+hs38  136 137    0.0000    
+hs39  138 139    0.0000    
+hs40  140 140    1.0000    
+hs41  146 147    0.0000    
+hs42  148 149    0.0000    
+hs43  150 151    0.0000    
+hs44  152 153    0.0000    
+hs45  154 155    1.0000    
+hs46  156 157    0.0000    
+hs47  158 160    0.0000    
+hs48  160 161    0.0000    
+hs49  162 163    1.0000    

cricos/circos-0.69-9/bin/data/hist copy.txt

@@ -0,0 +1,99 @@
+hs1   0   1      16.031300127999998,99.76126564639999,183.49123116479998,267.2211966832,350.95116220159997,434.68112771999995,518.4110932384,602.1410587567999,685.8710242751999,769.6009897936,853.3309553119999
+hs2   1   2      6.731,27.82690999999994,48.92281999999989,70.01872999999982,91.11463999999977,112.21054999999971,133.30645999999965,154.4023699999996,175.49827999999954,196.5941899999995,217.69009999999943
+hs3   3   4      0.0,26.867999999999995,53.73599999999999,80.60399999999998,107.47199999999998,134.33999999999997,161.20799999999997,188.07599999999996,214.94399999999996,241.81199999999995,268.67999999999995
+hs4   5   6      -7.571399999999989,-5.7753999999999905,-3.9793999999999925,-2.1833999999999945,-0.38739999999999597,1.4086000000000025,3.2046,5.0005999999999995,6.796599999999997,8.592599999999994,10.388599999999993
+hs5   7   8      0.0,2.3,4.6,6.8999999999999995,9.2,11.5,13.799999999999999,16.099999999999998,18.4,20.7,23.0
+hs6   9   10     1.0,7.1,13.2,19.299999999999997,25.4,31.5,37.599999999999994,43.699999999999996,49.8,55.9,62.0
+hs7   11  12     0.0,1.6,3.2,4.800000000000001,6.4,8.0,9.600000000000001,11.200000000000001,12.8,14.4,16.0
+hs8   13  14     0.0,1.1,2.2,3.3000000000000003,4.4,5.5,6.6000000000000005,7.700000000000001,8.8,9.9,11.0
+hs9   15  16     0.0,1.6,3.2,4.800000000000001,6.4,8.0,9.600000000000001,11.200000000000001,12.8,14.4,16.0
+hs10  17  18     8.0,40.0,72.0,104.0,136.0,168.0,200.0,232.0,264.0,296.0,328.0
+hs11  19  20     0.0,1.1,2.2,3.3000000000000003,4.4,5.5,6.6000000000000005,7.700000000000001,8.8,9.9,11.0 
+hs12  21  22     0.0,1.6,3.2,4.800000000000001,6.4,8.0,9.600000000000001,11.200000000000001,12.8,14.4,16.0
+hs13  23  24     0.0,0.8,1.6,2.4000000000000004,3.2,4.0,4.800000000000001,5.6000000000000005,6.4,7.2,8.0
+hs14  25  26     0.0,0.7,1.4,2.0999999999999996,2.8,3.5,4.199999999999999,4.8999999999999995,5.6,6.3,7.0
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cricos/circos-0.69-9/bin/data/labels.txt

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cricos/circos-0.69-9/bin/data/link.txt

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+var43  0 100 var3  0 100  color=lpgreen
+var43  0 100 var4  0 100  color=lpgreen
+var43  0 100 var6  0 100  color=lpgreen
+var43  0 100 var9  0 100  color=lpgreen
+var43  0 100 var13 0 100  color=lpgreen
+var43  0 100 var16 0 100  color=lpgreen
+var43  0 100 var17 0 100  color=lpgreen
+var43  0 100 var18 0 100  color=lpgreen
+var43  0 100 var19 0 100  color=lpgreen
+var43  0 100 var24 0 100  color=lpgreen
+var43  0 100 var27 0 100  color=lpgreen
+var43  0 100 var29 0 1400 color=lpgreen
+var43  0 100 var31 0 1200 color=lpgreen
+var43  0 100 var33 0 1000 color=lpgreen
+var43  0 100 var40 0 100  color=lpgreen
+var43  0 100 var41 0 100  color=lpgreen
+var43  0 100 var42 0 100  color=lpgreen
+var43  0 100 var1s 0 100  color=lpgreen
+
+var11  0 100 var2  0 100  color=vdpurple
+var11  0 100 var3  0 100  color=vdpurple
+var11  0 100 var4  0 100  color=vdpurple
+var11  0 100 var5  0 100  color=vdpurple
+var11  0 100 var9  0 100  color=vdpurple
+var11  0 100 var1  0 100  color=vdpurple
+var11  0 100 var12 0 100  color=vdpurple
+var11  0 100 var14 0 100  color=vdpurple
+var11  0 100 var17 0 100  color=vdpurple
+var11  0 100 var19 0 100  color=vdpurple
+var11  0 100 var21 0 300  color=vdpurple
+var11  0 100 var22 0 1300 color=vdpurple
+var11  0 100 var24 0 100  color=vdpurple
+var11  0 100 var26 0 100  color=vdpurple
+var11  0 100 var27 0 100  color=vdpurple
+var11  0 100 var28 0 100  color=vdpurple
+var11  0 100 var31 0 1200 color=vdpurple
+var11  0 100 var34 0 100  color=vdpurple
+var11  0 100 var39 0 100  color=vdpurple
+var11  0 100 var40 0 100  color=vdpurple
+var11  0 100 var41 0 100  color=vdpurple
+var11  0 100 var46 0 100  color=vdpurple

cricos/circos-0.69-9/bin/data/link2.txt

@@ -0,0 +1,93 @@
+var44  0 100 var36 0 300 color=vdgrey
+var44  0 100 var20 0 100 color=vdgrey
+var44  0 100 var45 0 100 color=vdgrey
+var44  0 100 var47 0 100 color=vdgrey
+var44  0 100 var48 0 100 color=vdgrey
+var44  0 100 var49 0 100 color=vdgrey
+
+var10  0 100 var25 0 100 color=black
+var10  0 100 var30 0 1000 color=black
+
+var34  0 100 var2   0 100  color=lpred
+var34  0 100 var3   0 100  color=lpred
+var34  0 100 var4   0 100  color=lpred
+var34  0 100 var5   0 100  color=lpred
+var34  0 100 var8   0 100  color=lpred
+var34  0 100 var11  0 100  color=lpred
+var34  0 100 var13  0 100  color=lpred
+var34  0 100 var14  0 100  color=lpred
+var34  0 100 var16  0 100  color=lpred
+var34  0 100 var17  0 100  color=lpred
+var34  0 100 var18  0 100  color=lpred
+var34  0 100 var19  0 100  color=lpred
+var34  0 100 var21  0 300  color=lpred
+var34  0 100 var23  0 100  color=lpred
+var34  0 100 var27  0 100  color=lpred
+var34  0 100 var32  0 1100 color=lpred
+var34  0 100 var33  0 1000 color=lpred
+var34  0 100 var1   0 100  color=lpred
+var34  0 100 var37  0 200  color=lpred
+var34  0 100 var38  0 100  color=lpred
+var34  0 100 var40  0 100  color=lpred
+var34  0 100 var42  0 100  color=lpred
+
+var19  0 100 var2  0 100  color=lpblue
+var19  0 100 var3  0 100  color=lpblue
+var19  0 100 var4  0 100  color=lpblue
+var19  0 100 var7  0 100  color=lpblue
+var19  0 100 var8  0 100  color=lpblue
+var19  0 100 var9  0 100  color=lpblue
+var19  0 100 var12 0 100  color=lpblue
+var19  0 100 var15 0 100  color=lpblue
+var19  0 100 var18 0 100  color=lpblue
+var19  0 100 var1  0 100  color=lpblue
+var19  0 100 var23 0 100  color=lpblue
+var19  0 100 var28 0 100  color=lpblue
+var19  0 100 var33 0 1000 color=lpblue
+var19  0 100 var34 0 100  color=lpblue
+var19  0 100 var35 0 100  color=lpblue
+var19  0 100 var38 0 100  color=lpblue
+var19  0 100 var39 0 100  color=lpblue
+
+var43  0 100 var2  0 100  color=lpgreen
+var43  0 100 var3  0 100  color=lpgreen
+var43  0 100 var4  0 100  color=lpgreen
+var43  0 100 var6  0 100  color=lpgreen
+var43  0 100 var9  0 100  color=lpgreen
+var43  0 100 var13 0 100  color=lpgreen
+var43  0 100 var16 0 100  color=lpgreen
+var43  0 100 var17 0 100  color=lpgreen
+var43  0 100 var18 0 100  color=lpgreen
+var43  0 100 var19 0 100  color=lpgreen
+var43  0 100 var24 0 100  color=lpgreen
+var43  0 100 var27 0 100  color=lpgreen
+var43  0 100 var29 0 1400 color=lpgreen
+var43  0 100 var31 0 1200 color=lpgreen
+var43  0 100 var33 0 1000 color=lpgreen
+var43  0 100 var40 0 100  color=lpgreen
+var43  0 100 var41 0 100  color=lpgreen
+var43  0 100 var42 0 100  color=lpgreen
+var43  0 100 var1s 0 100  color=lpgreen
+
+var11  0 100 var2  0 100  color=vdpurple
+var11  0 100 var3  0 100  color=vdpurple
+var11  0 100 var4  0 100  color=vdpurple
+var11  0 100 var5  0 100  color=vdpurple
+var11  0 100 var9  0 100  color=vdpurple
+var11  0 100 var1  0 100  color=vdpurple
+var11  0 100 var12 0 100  color=vdpurple
+var11  0 100 var14 0 100  color=vdpurple
+var11  0 100 var17 0 100  color=vdpurple
+var11  0 100 var19 0 100  color=vdpurple
+var11  0 100 var21 0 300  color=vdpurple
+var11  0 100 var22 0 1300 color=vdpurple
+var11  0 100 var24 0 100  color=vdpurple
+var11  0 100 var26 0 100  color=vdpurple
+var11  0 100 var27 0 100  color=vdpurple
+var11  0 100 var28 0 100  color=vdpurple
+var11  0 100 var31 0 1200 color=vdpurple
+var11  0 100 var34 0 100  color=vdpurple
+var11  0 100 var39 0 100  color=vdpurple
+var11  0 100 var40 0 100  color=vdpurple
+var11  0 100 var41 0 100  color=vdpurple
+var11  0 100 var46 0 100  color=vdpurple

cricos/circos-0.69-9/bin/gddiag

@@ -0,0 +1,634 @@
+#!/bin/env perl
+
+=pod
+
+=head1 NAME
+
+gddiag - short GD diagnostics
+
+=head1 SYNOPSIS
+
+  # organize color swatches in 10 columns, each column swatch
+  # 20 pixels in size and color labels size 8
+  gddiag -conf etc/gddiag.conf -output_file_root gdtest [-debug] [-help] [-man]
+
+=head1 DESCRIPTION
+
+This script helps diagnose any problems with gd and Perl's GD
+module. It generates a matrix of colored squares, some rotated lines
+(with and without antialiasing) and text for each font defined in the
+<fonts> block.
+
+=head1 LIMITATIONS
+
+As of the current release of gd (2.0.35), antialiasing is not
+supported for lines with (a) thickness > 1 or (b) color with alpha
+channel. Therefore, if you want lines with transparency (e.g. 50%
+opaque), or lines whose thickness is greater than 1, you must give up
+antialiasing. Antialiasing with thick lines is planned in gd 2.1.0 -
+see
+
+http://bugs.libgd.org/?do=details&task_id=65&histring=antialias
+
+One way to "add" antialiasing, is to create an image that is 2x the
+size of the desired final result and then shrink the image with a tool
+like ImageMagick's 'convert'.
+
+=head1 HISTORY
+
+=over
+
+=item * 16 June 2009 v0.14
+
+Removed dependence on tutorial configuration file by adding a dedicated configuration file.
+
+=item * 3 Mar 2009 v0.13
+
+Added -alpha.
+
+=item * 30 Sep 2008 v0.12
+
+Added column number and width
+
+=item * 16 Apr 2008 v0.11
+
+Added labels sampling defined fonts
+
+=item * 25 Feb 2008 v0.10
+
+Started and versioned
+
+=back
+
+=head1 BUGS
+
+Please report all bugs, feature requests and general comments to Martin Krzywinski (martink@bcgsc.ca).
+
+=head1 AUTHOR
+
+Martin Krzywinski
+martink@bcgsc.ca
+mkweb.bcgsc.ca
+
+=head1 CONTACT
+
+  Martin Krzywinski
+  Genome Sciences Centre
+  Vancouver BC Canada
+  www.bcgsc.ca
+  martink@bcgsc.ca
+
+=cut
+
+################################################################
+#
+# Copyright 2004-2011 Martin Krzywinski
+#
+# This file is part of the Genome Sciences Centre Perl code base.
+#
+# This script is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This script is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this script; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+################################################################
+
+use strict;
+use constant twoPI   => 6.283185307;
+use constant deg2rad => 0.0174532925;
+use constant rad2deg => 57.29577951;
+use constant PI      => 3.141592654;
+use constant PIover2 => 1.570796327;
+use Carp;
+use Config::General;
+use Data::Dumper;
+use File::Basename;
+use FindBin;
+use Getopt::Long;
+use IO::File;
+use Math::Round;
+use Math::VecStat qw(sum min max average);
+use POSIX qw(atan ceil);
+use Pod::Usage;
+use Set::IntSpan 1.11 qw(map_set);
+use Storable;
+use Time::HiRes qw(gettimeofday tv_interval);
+use GD;
+
+use lib "$FindBin::RealBin";
+use lib "$FindBin::RealBin/../lib";
+use lib "$FindBin::RealBin/lib";
+
+use Circos::Configuration qw(%CONF $DIMS);
+use Circos::Colors;
+
+our %OPT;
+
+GetOptions(\%OPT,
+	   "colsize=i",
+	   "alpha",
+	   "verbose+",
+	   "output_file_root=s",
+	   "configfile=s","help","man","debug+");
+
+pod2usage() if $OPT{help};
+pod2usage(-verbose=>2) if $OPT{man};
+loadconfiguration($OPT{configfile});
+populateconfiguration(); # copy command line options to config hash
+validateconfiguration(); 
+if($CONF{debug} > 1) {
+  $Data::Dumper::Pad = "debug parameters";
+  $Data::Dumper::Indent = 1;
+  $Data::Dumper::Quotekeys = 0;
+  $Data::Dumper::Terse = 1;
+  print Dumper(\%CONF);
+}
+
+my $dims;
+
+# generate rows and columns of color patches
+
+my $seen_color;
+my $layout  = get_layout();
+
+my ($im,$colors) = make_image($layout);
+
+my ($x,$y) = ($CONF{marginx},$CONF{marginy});
+for my $row (@$layout) {
+    for my $data (@$row) {
+	if($data->{label}) {
+	    $im->string(gdTinyFont,$x,$y,$data->{label},$colors->{black});
+	    $x += 6 * length($data->{label});
+	} elsif ( $data->{type} eq "color") {
+	    if($CONF{alpha}) {
+		for my $alpha (reverse 0..5) {
+		    my $color = $colors->{ $data->{name} . "_a$alpha" };
+		    my $f = 1 - 0.8*(5-$alpha)/5;
+		    $im->filledRectangle($x,$y,
+					 $x+$CONF{colsize}*$f,$y+$CONF{colsize}*$f,
+					 $color);
+		}
+	    } else {
+		my $color = $colors->{ $data->{name} };
+		$im->filledRectangle($x,$y,
+				     $x+$CONF{colsize},$y+$CONF{colsize},
+				     $color);
+	    }
+	    $im->rectangle($x,$y,
+			   $x+$CONF{colsize},$y+$CONF{colsize},
+			   $colors->{ vlgrey });
+	    $x += $CONF{colsize} + $CONF{colmargin};
+	} elsif ($data->{type} eq "font") {
+	    $im->stringFT($colors->{black},
+			  locate_file($CONF{fonts}{ $data->{font}}),
+			  $CONF{fontsize},
+			  0,
+			  $x,$y+$CONF{fontsize},
+			  join("", map {chr(97+$_)} (0..25)));
+	    $y += $CONF{fontsize} * 0.75;
+	} else {
+	    $x += $CONF{colmargin};
+	}
+    }
+    $x  = $CONF{marginx};
+    $y += $CONF{colsize} + $CONF{colmargin};
+}
+
+my $output_file = sprintf("%s.png",$CONF{output_file_root});
+open(PNG,">$output_file") || confess "cannot open output file $output_file";
+binmode PNG;
+print PNG $im->png;
+close(PNG);
+printinfo("Created color diagnostic image at $output_file");
+printinfo("GD version",$GD::VERSION);
+
+exit;
+
+sub get_layout {
+    my $color_layout = get_color_layout();
+    my $font_layout  = get_font_layout();
+    return [grep($_, @$color_layout,@$font_layout)];
+}
+
+sub get_font_layout {
+    my @fonts = sort keys %{$CONF{fonts}};
+    my $font_layout;
+    for my $font (@fonts) {
+	push @$font_layout, [ {label=>sprintf("font %13s",$font) }, { font=>$font, type=>"font" } ];
+    }
+    return $font_layout;
+
+}
+sub get_color_layout {
+    my @colors = keys %{$CONF{colors}};
+    my @layout;
+    # brewer palettes
+    my $brewer_palettes = make_brewer(@colors);
+    for my $type (sort keys %$brewer_palettes) {
+	for my $palette (sort keys %{$brewer_palettes->{$type}}) {
+	    push @layout, [{label=>sprintf("%13s","$palette-$type")}];
+	    for my $ncolors (sort {$a <=> $b} keys %{$brewer_palettes->{$type}{$palette}}) {
+		push @{$layout[-1]}, {label=>$ncolors};
+		for my $idx (sort {$a <=> $b} keys %{$brewer_palettes->{$type}{$palette}{$ncolors}}) {
+		    my $color_data = $brewer_palettes->{$type}{$palette}{$ncolors}{$idx};
+		    push @{$layout[-1]}, $color_data;
+		    $seen_color->{$color_data->{name}}++;
+		}
+		push @{$layout[-1]}, undef;
+	    }
+	}
+    }
+    # chromosomes
+    my $chr_palettes = make_chr(@colors);
+    for my $type (sort keys %$chr_palettes) {
+	push @layout, [{label=>sprintf("%13s",$type)}];
+	for my $color (sort {$a->{label} <=> $b->{label} || $a->{label} cmp $b->{label}} @{$chr_palettes->{$type}}) {
+	    push @{$layout[-1]}, {label=>$color->{label} || "''"};
+	    push @{$layout[-1]}, {name=>$color->{name}, type=>"color",rgb=>$color->{rgb}};
+	    $seen_color->{$color->{name}}++;
+	}
+    }
+    # other colors
+    my $other_palettes = make_other_palette(@colors);
+    for my $type (sort keys %$other_palettes) {
+	push @layout, [{label=>sprintf("%13s",$type)}];
+	for my $color (sort {$a->{idx} <=> $b->{idx}} @{$other_palettes->{$type}}) {
+	    push @{$layout[-1]}, {label=>$color->{label} || "''"};
+	    push @{$layout[-1]}, {name=>$color->{name}, type=>"color",rgb=>$color->{rgb}};
+	}
+    }
+    return \@layout;
+}
+
+sub make_other_palette {
+    my $other_palettes;
+    for my $color (@_) {
+	if($color =~ /^(v*(l|d))(.+)$/) {
+	    my ($prefix,$name) = ($1,$3);
+	    next if $seen_color->{$color};
+	    next if $color =~ /-(qual|seq|div)/;
+	    my $idx = 0;
+	    if($color =~ /^(v*)(d|l)/) {
+		if($2 eq "d") {
+		    $idx += length($1) + 10;
+		} else {
+		    $idx -= length($1);
+		}
+	    }
+	    push @{$other_palettes->{$name}}, {rgb=>[split(",",$CONF{colors}{$color})],
+					       idx=>$idx,
+					       label=>$prefix,
+					       name=>$color};
+	}
+    }
+    return $other_palettes;
+}
+sub make_chr {
+    my $chr_palettes;
+    my @type = qw(chr gpos gneg gvar acen stalk);
+    for my $type (@type) {
+	for my $color (@_) {
+	    if($color =~ /$type/) {
+		if($color =~ /^(.*$type)(.*)/) {
+		    my ($palette,$label) = ($1,$2);
+		    next unless $CONF{colors}{$color} =~ /,/;
+		    push @{$chr_palettes->{$palette}}, {rgb=>[split(",",$CONF{colors}{$color})],
+							name=>$color,
+							label=>$label};
+		}
+	    }
+	}
+    }
+    return $chr_palettes;
+}
+
+sub make_brewer {
+    my @types = qw(seq div qual);
+    my $typerx = join("|",@types);
+    my @colors = sort grep($_ =~ /-($typerx)-/, @_);
+    my $brewer_palettes;
+    for my $type (@types) {
+	my @colors_type = grep($_ =~ /-$type-/, @colors);
+	for my $color (@colors_type) {
+	    if($color =~ /^(.+)-(\d+)-$type-(\d+)/) {
+		my ($palette,$ncolors,$idx) = ($1,$2,$3);
+		my @rgb = split(",",$CONF{colors}{$color});
+		$brewer_palettes->{$type}{$palette}{$ncolors}{$idx} = {name=>$color,rgb=>\@rgb,type=>"color"};
+	    }
+	}
+    }
+    return $brewer_palettes;
+}
+
+sub make_image {
+    my $layout = shift;
+    my $nrows  = @$layout;
+    my $ncols  = max( map {int(@$_)} @$layout);
+    my ($height,$width) = (2*$CONF{marginy},2*$CONF{marginx});
+    my @widths;
+    for my $row (@$layout) {
+	$height += $CONF{colsize} + $CONF{colmargin};
+	push @widths, 0;
+	for my $col (@$row) {
+	    if($col->{label}) {
+		$widths[-1] += 6 * length($col->{label});
+	    } elsif ($col->{type} eq "color") {
+		$widths[-1] += $CONF{colsize} + $CONF{colmargin};
+	    } elsif ($col->{type} eq "font") {
+		$height += $CONF{fontsize};
+	    } else {
+		$widths[-1] += $CONF{colmargin};
+	    }
+	}
+    }
+    $width += max(@widths);
+    my $im  = GD::Image->new($width,$height,1);
+    #printinfo("created image",$width,$height);
+    if(! $im) {
+	die "There was a problem creating a 24-bit image. This is a fatal error and you will not be able to use transparency in Circos. The error is likely due to a problem with Perl's GD module. Your installed version is ($GD::VERSION). See http://search.cpan.org/dist/GD/GD.pm for the latest version and upgrade, or fix your installation.";
+    }
+    $im->alphaBlending(1);
+    my $colors = Circos::Colors::allocate_colors($im);
+    printinfo("allocated",int(keys %$colors),"colors");
+    $im->fill(0,0,$colors->{white});
+    return ($im,$colors);
+}
+
+exit;
+
+# how many colors are defined?
+my $ncolors = keys %{$CONF{colors}};
+# how many fonts are defined?
+my $nfonts  = keys %{$CONF{fonts}};
+# how many rows of color swatches?
+my $nrow = ceil($ncolors / $CONF{ncol});
+# how wide is the image?
+my $width = $CONF{ncol} * 2*$CONF{colsize} + $CONF{colsize} + 2*$CONF{marginx};
+# how tall is the image?
+my $height = (1+$nrow) * 2*$CONF{colsize} + $nfonts * 2.5*$CONF{labelsize} + 2*$CONF{marginy};
+
+printinfo("allocating image",$width,$height);
+
+# try to create an 8bit image
+my $im8 = GD::Image->new($width,$height);
+# try to create a 24bit image
+my $im  = GD::Image->new($width,$height,1);
+if(! $im) {
+  die "There was a problem creating a 24-bit image. This is a fatal error and you will not be able to use transparency in Circos. The error is likely due to a problem with Perl's GD module. Your installed version is ($GD::VERSION). See http://search.cpan.org/dist/GD/GD.pm for the latest version and upgrade, or fix your installation.";
+}
+$im->alphaBlending(1);
+my $colors = Circos::Colors::allocate_colors($im);
+printinfo("allocated",int(keys %$colors),"colors");
+$im->fill(0,0,$colors->{white});
+
+my $swatch_idx    = 0;
+my $swatch_stroke = 1;
+
+map { delete $colors->{$_} if ref $colors->{$_} } keys %$colors;
+
+for my $color_strings (sort { (($b->[1] eq "chr") - ($a->[1] eq "chr")) || $a->[1] cmp $b->[1] || $a->[2] <=> $b->[2] } map { [$_,($_ =~ /v*[ld]*(.+?)\d*$/g),($_ =~ /(\d+)$/g)] } 
+		       grep($_ !~ /_a\d+/, keys %$colors)) {
+  my ($color,$color_stem,$color_dig) = @$color_strings;
+  next if $color =~ /(seq|div|qual)/ && $color =~ /-[a-z]$/;
+  #my $brushc = $colors->{"d$color_stem"} ? "d$color_stem" : "black";
+  #my ($brush,$brushcolor) = init_brush($swatch_stroke,$swatch_stroke,$brushc);
+  my ($x,$y) = ( $CONF{marginx}+($swatch_idx % $CONF{ncol})*2*$CONF{colsize},
+		 $CONF{marginy}+int($swatch_idx/$CONF{ncol})*2*$CONF{colsize} );
+
+  for my $i (0..10) {
+    $im->filledRectangle($x+3*$i,$y-$CONF{colsize}/4,
+			 $x+3*$i+2,$y-$CONF{colsize}/5,
+			 $colors->{$color . "_a$i"});
+  }
+
+  $im->filledRectangle($x,$y,
+		       $x+$CONF{colsize},$y+$CONF{colsize},
+		       $colors->{$color});
+  #$im->setBrush($brush);
+  $im->rectangle($x,$y,
+		 $x+$CONF{colsize},$y+$CONF{colsize},
+		 $colors->{black});
+  my $text_size = $CONF{labelsize} || 0.4*$CONF{colsize};
+  my $text = $color;
+  $text =~ s/-(seq|div|qual|)-/-/;
+  $im->stringFT($colors->{black},
+		locate_file($CONF{fonts}{mono} || $CONF{fonts}{default}),
+		$text_size,
+		0,
+		$x,$y + $CONF{colsize} + $text_size + 2,
+		$text);
+  $swatch_idx++;
+}
+
+my ($x,$y) = ($CONF{marginx},$CONF{marginy}+(1+$nrow)*2*$CONF{colsize});
+for my $font (keys %{$CONF{fonts}}) {
+  printinfo("drawing font",$font,"from file",locate_file($CONF{fonts}{$font}));
+  $im->stringFT($colors->{black},
+		locate_file($CONF{fonts}{$font}),
+		2*$CONF{labelsize},
+		0,
+		$x,$y,
+		$font);
+  $y += 2.5*$CONF{labelsize};
+}
+
+# draw some lines
+
+($x,$y) = (2*$CONF{marginx},$CONF{marginy}+($nrow)*2*$CONF{colsize});
+my $len = 10;
+my $step = $len*sqrt(2);
+for my $i (0..36) {
+  $im->filledArc($x,$y,$len,$len,0,360,$colors->{red});
+  $im->filledArc($x,$y+$step,$len,$len,0,360,$colors->{red});
+  $im->filledArc($x,$y+2*$step,$len,$len,0,360,$colors->{red});
+  $x+= $step;
+}
+
+($x,$y) = (2*$CONF{marginx},$CONF{marginy}+($nrow)*2*$CONF{colsize});
+for my $i (0..36) {
+  my $angle = $i*10;
+  $im->setAntiAliased($colors->{black});
+  $im->line($x - $len*cos($angle*deg2rad),
+	    $y - $len*sin($angle*deg2rad),
+	    $x + $len*cos($angle*deg2rad),
+	    $y + $len*sin($angle*deg2rad),
+	    gdAntiAliased);
+  $im->line($x - $len*cos($angle*deg2rad),
+	    $y + $step - $len*sin($angle*deg2rad),
+	    $x + $len*cos($angle*deg2rad),
+	    $y + $step + $len*sin($angle*deg2rad),
+	    $colors->{black});
+
+  my $alpha = $i % 11;
+  my $thickness = 1 + ($i % 4);
+  my $color = "black_a".$alpha;
+
+  $im->setThickness($thickness);
+  $im->line($x - $len*cos($angle*deg2rad),
+	    $y + 2*$step - $len*sin($angle*deg2rad),
+	    $x + $len*cos($angle*deg2rad),
+	    $y + 2*$step + $len*sin($angle*deg2rad),
+	    $colors->{$color});
+  $im->setThickness(1);
+  $x += $step;
+}
+
+my $outputfile = $CONF{output_file};
+open(PNG,">$outputfile") || confess "cannot open output file $outputfile";
+binmode PNG;
+print PNG $im->png;
+close(PNG);
+printinfo("created gd diagnostic image at $outputfile");
+printinfo("used GD version",$GD::VERSION);
+
+sub init_brush {
+  my ($w,$h,$brush_color) = @_;
+  $h ||= $w;
+  my $brush = new GD::Image($w,$h);
+  my $color = Circos::Colors::allocate_colors($brush);
+  if($brush_color && $color->{$brush_color}) {
+    $brush->fill(0,0,$color->{$brush_color});
+  }
+  return ($brush,$color);
+}
+
+sub locate_file {
+  my $file = shift;
+  $file =~ s/,.*//;
+  if(-e $file && -r _) {
+    return $file;
+  } elsif (-e $file && ! -r _) {
+    confess "file $file exists, but cannot be read";
+  } else {
+    # look for the file elsewhere
+    for my $dir ( 
+		 "$FindBin::RealBin/",
+		 "$FindBin::RealBin/etc",
+		 "$FindBin::RealBin/../etc",
+		 "$FindBin::RealBin/../",
+		 "$FindBin::RealBin/../etc",
+		 "$FindBin::RealBin/../../etc",
+		) {
+      printwarning("trying $dir/$file");
+      if(-e "$dir/$file" && -r "$dir/$file") {
+	printwarning("$file found in $dir/$file");
+	return "$dir/$file";
+      }
+    }
+  }
+  confess "could not locate $file";
+}
+
+################################################################
+#
+# *** DO NOT EDIT BELOW THIS LINE ***
+#
+################################################################
+################################################################
+################################################################
+################################################################
+
+sub validateconfiguration {
+  for my $parsekey (keys %CONF) {
+    if($parsekey =~ /^(__(.+)__)$/) {
+      if(! defined $CONF{$1}) {
+	confess "ERROR - problem in configuration file - you want to use variable $1 ($2) in another parameter, but this variable is not defined";
+      }
+      my ($token,$parsevalue) = ($1,$CONF{$1});
+      for my $key (keys %CONF) {
+	$CONF{$key} =~ s/$token/$parsevalue/g;
+      }
+    }
+  }
+  confess "error - no configuration file specified - please use -conf FILE" unless $CONF{configfile};
+
+  if($CONF{alpha}) {
+    die "value passed to -alpha must be 0-126" unless $CONF{alpha} >=0 && $CONF{alpha} <= 127;
+  }
+  $CONF{image}{pngmake} = 1;
+
+}
+
+sub populateconfiguration {
+  foreach my $key (keys %OPT) {
+    $CONF{$key} = $OPT{$key};
+  }
+
+  # any configuration fields of the form __XXX__ are parsed and replaced with eval(XXX). 
+  # The configuration can therefore depend on itself.
+  #
+  # flag = 10
+  # note = __2*$CONF{flag}__ # would become 2*10 = 20
+
+  repopulateconfiguration(\%CONF);
+
+  # populate some defaults
+
+}
+
+sub repopulateconfiguration {
+  my $root     = shift;
+  for my $key (keys %$root) {
+    my $value = $root->{$key};
+    if(ref($value) eq "HASH") {
+      repopulateconfiguration($value);
+    } else {
+      while($value =~ /__([^_].+?)__/g) {
+	my $source = "__" . $1 . "__";
+	my $target = eval $1;
+	$value =~ s/\Q$source\E/$target/g;
+      }
+      $root->{$key} = $value;
+    }
+  }
+}
+
+sub loadconfiguration {
+  my $file = shift;
+  my ($scriptname) = fileparse($0);
+  if(-e $file && -r _) {
+    # great the file exists
+  } elsif (-e "/home/$ENV{LOGNAME}/.$scriptname.conf" && -r _) {
+    $file = "/home/$ENV{LOGNAME}/.$scriptname.conf";
+  } elsif (-e "$FindBin::RealBin/$scriptname.conf" && -r _) {
+    $file = "$FindBin::RealBin/$scriptname.conf";
+  } elsif (-e "$FindBin::RealBin/etc/$scriptname.conf" && -r _) {
+    $file = "$FindBin::RealBin/etc/$scriptname.conf";
+  } elsif (-e "$FindBin::RealBin/../etc/$scriptname.conf" && -r _) {
+    $file = "$FindBin::RealBin/../etc/$scriptname.conf";
+  } else {
+    confess "error - could not find the configuration file [$file]";
+  }
+  $OPT{configfile} = $file;
+  my $conf = new Config::General(-ConfigFile=>$file,
+				 -AllowMultiOptions=>1,
+				 -LowerCaseNames=>1,
+				 -ConfigPath=>["$FindBin::RealBin/etc","$FindBin::RealBin/../etc","$FindBin::RealBin/..",$FindBin::RealBin,dirname($file),"$FindBin::RealBin/../".dirname($file)],
+				 -AutoTrue=>1);
+  %CONF = $conf->getall;
+}
+
+sub printdebug {
+  printinfo("debug",@_) if $CONF{debug};
+}
+
+sub printwarning {
+  printinfo("warning",@_) if $CONF{warnings};
+}
+
+sub printinfo {
+  print join(" ",@_),"\n";
+}
+
+sub printdumper {
+    printinfo(Dumper(@_));
+}

cricos/circos-0.69-9/bin/list.modules

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+# Contributed by Charles Howes
+# http://groups.google.com/group/circos-data-visualization/browse_thread/thread/96e74d863a53e405?hl=en_US
+awk '!/^[\t ]*use /{next};$2~/^(lib|Circos.*|base|strict|vars|warnings);?$/{next};{sub(";","",$2);print $2}' circos ../lib/Circos/*pm ../lib/Circos.pm ../lib/Circos/*/*pm | sort -u 

cricos/circos-0.69-9/bin/test.modules

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+echo "Circos can now list its own modules."
+echo
+echo "> circos -modules"

cricos/circos_readme.txt

@@ -0,0 +1,23 @@
+# 1. Verify Strawberry Perl installation
+perl --version
+
+# 2. Check Circos module dependencies
+perl circos -modules
+
+# 3. Auto-install missing modules
+perl -e "$output = `perl circos -modules`; while($output =~ /missing\s+(\S+)/g) { system('cpan', $1); }"
+
+# [Alternative: Manual module installation]
+# perl -MCPAN -e shell
+# install Module::Name
+# exit
+
+# 4. Diagnose GD library
+perl gddiag
+
+# 5. Run Circos
+circos -conf circos.cnf
+
+# [If paranoid error occurs]
+# Use this only when you get a paranoid-specific error
+circos -noparanoid -conf circos.cnf

result/1_standard_ML/failed/AqSolDB/failed_smiles.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fbb676c7f42df05a6c87fa43cbc3ad1db0c8b90161f2204d5a3ba2dc837beae2
+size 4259