Tuesday, 5 June 2012

Circos v0.61 released

From: "Martin" <martin.krzywinski
Date: Jun 5, 2012 8:28 AM
Subject: [circos] Circos v0.61 released

I've release v0.61 and the accompanying tutorials. 

There are quite a few changes in this version. The major ones are <axes> and <backgrounds>. With this change, old configurations files that had axis_* parameters will not work.

Please note that top-level blocks like <colors> will now be automatically merged. This should make it easier for you to override parameters in blocks that are being included from other files.

Also of note is the addition of conf(.,VAR) to access the value of VAR in the current block. This makes it easier to define a configuration file parameter based on the value of another.

I realize that the online tutorial descriptions are starting to drift away from all the newly added features. For the next while, my focus will be to bring the documentation up-to-date.


v0.61 CHANGES 

Identified a bug in gd that causes problems when lines of thickess 1px are anti-aliased. Added anti_aliasing parameter to turn aa off to mitigate this.

Fixed bug that caused elements in list defined by chromosomes_colors to be applied in the wrong order.

Fixed a bug that made backgrounds to be incorrectly oriented for tracks whose orientation is reversed.

Added skip_missing_expression_vars in etc/housekeeping.conf to allow skipping references to missing parameters with var(NAME).

Added label_format to <ideogram> block. This parameter allows you to use the same dynamic syntax for labels as you do for rules.

  label_format = eval(var(chr))
  label_format = eval(var(chr_with_tag))
  label_format = eval(sprintf("%s %.3fMb",var(chr),var(size)/1e6))

Changed rebuild_color_cache to color_cache_rebuild.

Track axes are now defined using <axes> blocks with one or more <axis> entries. Each block can contain one or more of the following parameters: color, thickness, spacing, position, position_skip. Spacing and position parameters can be relative (use r suffix).

   color = grey
   thickness = 1
   spacing = 0.1r 
   position_skip = 25000
   position = 0.35r
   color = red

Track background is now defined using <backgrounds> blocks with one or more <background> entries. Each block can contain one or more of the following parameters: color, stroke_{color|thickness}, y0, y1. If y0 and/or y1 are not specified, track minimum and maximum are used, respectively. y0 and y1 can be absolute or relative (use r suffix for relative).

   color = lgrey
   y0 = 0.5r
   color = lgred
   y1 = 0.5r
   color = lgreen

When cytogenetic bands overlap, a warning is produced instead of fatal error.

Adjusted code which made v6.0 incompatible with perl 5.8 due to a recursive regular expression used to parse rules. Text::Balanced is now used to extract function arguments in balanced parentheses.

Added conf(.,x) syntax to access value of 'x' in the current block.

  r0 = 0.8r
  r1 = conf(.,r0)+0.1r

Top level blocks, such as <ideogram>, <colors>, <fonts>, <image> and <ticks> are merged. This allows you to do something like this

  # define your own color(s)
  mycolor = 255,100,100

  # include default color, fonts and patterns, which brings in 
  # <colors>, <fonts> and <patterns> blocks
  <<include etc/colors_fonts_patterns.conf>>

To override a value, don't forget to use *. For example, to hide the ideogram label in tutorial 2.2,

  # * is required at the end of parameter name so that it overrides the
  # default value of 'show_label' defined in the block imported below
  show_label* = no
  # default <ideogram> block from file
  <<include ideogram.conf>>

snuggle_sampling can now be relative

  max_snuggle_distance = 1r
  snuggle_sampling = 0.2r

Text that is not placed can now be explicitly shown using 'overflow'. This text will be placed at r0 of the track. The format of the unplaced text can be controled using overflow_* parmaeters

  overflow       = show
  overflow_font  = bold
  overflow_size  = 36
  overflow_color = red

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