Monday, 6 February 2012

[circos] Circos v0.56 released

---------- Forwarded message ----------
From: "Martin"
Date: Feb 6, 2012 9:56 am
Subject: [circos] Circos v0.56 released

Dear Circos users!

I have made v0.56 available.

Thank you to everyone who submitted bug reports and patiently waited
for me to respond.

Remember that now tutorials and the core code are kept separate. The
core circos-0.56.tgz archive contains an example directory (example/)
that creates a relatively complex image. Use this to ensure that
everything is working.

Most of the changes are bug fixes. Error handling is improved - many
errors have a gentler format and should be more explanatory.


1. Import colors/fonts/patterns all at once

Use a single line to add color, font and pattern definitions in

<<include etc/colors_fonts_patterns.conf>>

instead of

<<include etc/colors.conf>>

Note that colors.conf now imports brewer.conf automatically.

Please see example/etc/circos.conf for ideas of how to make your
configuration more modular.

2. Make sure you're using etc/housekeeping.conf

A while back, I had centralized system parameters that used to appear
at the bottom of circos.conf into a separate file. For those of you
who still have these parameters in their circos.conf file, please
remove them.

<<include etc/housekeeping.conf>>

instead of

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no
units_ok = bupr
units_nounit = n

3. Use debug_group

You'll notice that Circos' default debug output contains more text. By
default debugging that falls into the 'summary' category is created. A
complete list of debug categories is listed here

In particular, the following are very useful

  timer - show code timings
  io - loading and locating files
  textplace - reports whether a text in a text track has been
successfully placed

4. SVG text handling improved

I've revamped how SVG text labels are placed. You'll notice that fonts
now have font family definitions in etc/fonts.conf. This string is
used in the SVG file to specify the font. Once you have the font
installed on your system, labels won't all appear in the SVG app or
viewer default (e.g. Arial) font.

There's still more to do here, but it's getting better.


Parallel ideogram labels are now centered with respect to the

restrict_parameter_names now controls whether parameters are
restricted to a pre-defined list (e.g. color, thickness, etc). If you
have custom parameters (e.g. 'myspecialcode') then set
restrict_parameter_names=no. By default, this is always set to 'yes'.

Added link_orientation for text tracks. When set to "out" links from
text labels face out, rather than in.

Added font names to SVG files via font-family tag.

Removed -verbose. The -v flag now reports version.

Removed dependence on Graphics::ColorObject.

Added error handling framework.

Circos now requires Text::Format

Bug fix to heat map color mapping of last color.

Fixed bug which was causing line links to be drawn with a thickness
half of what was requested.

Fixed bug that prevented parameters made acceptable by the
restrict_parameter_names=no setting from being parsed.

Configuration file location is now guessed if guess_conf_location=yes
(see etc/housekeeping.conf)

Color file cache can now be static (color_cache_static) and dir/file
can be changed (color_cache_{file,dir})

Added 'placed' and 'not_placed' output for labels in text tracks to.
Use -debug_group text to see this.

  # create data file of labels that were not placed
  circos -conf ... -debug_group text | grep not_placed >

Parts of the code were made faster (unit checking) through Memoize.

Fixed a bug which prevented links with thickness=1 from being shown
with correct transparency.

Fixed bug in which color errors were produced when PNG file was not
asked for.

Fixed bug in which opacity of links in SVG files was missing in some

Fixed but which was assigning the wrong color to transparent links in
PNG files in some cases.

Centralized color configuration files colors.conf now includes
brewer.conf - no need to include brewer.conf separately.

Added -paranoid flag to exit on warnings.

Made error messages friendlier. Revamped internal error handling

Added data_path to allow adding to locations where files are searched

Added data/ to prefix path of locations where files are searched for.
Now the default search locations are

 { CWD | CIRCOS_PATH } + { . | .. | ../.. } + { . | etc | data }

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