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7 Mar 2005 - v0.1
24 May 2005 - v0.2
A large number of changes. Primarily
- support for non-linear scale
- support for optional tick labels and minimum tick separation
- reworked 2D data file formats
A lot of bugs fixed. Primarily
- fixed poor text layout on tick labels
- fixed support for newer GD (stringFT vs stringTTF)
25 May 2005 - v0.21
Added global scaling, described in Tutorial 6.
23 Jan 2007 - v0.22
Focused tutorials on figures in NYT article. Added support for multiple fonts. You no longer need to define $FONT yourself.
17 Oct 2007 - v0.31pre0
Prelease of 0.31. Nearly everything has been revamped.
Revamped configuration syntax, making it more intuitive and consistent.
New tutorials posted. Axes breaks added. More flexible ideogram ordering.
Significant changes to placement of data elements, now with support for relative and absolute position values.
18 Oct 2007 - v0.31pre1
Fixed memory problem when drawing highlights. Now require Set::IntSpan v1.11 or newer.
Additional sanity checks when loading configuration files.
23 Oct 2007 - v0.31pre2
Added tiles and heatmaps.
26 Oct 2007 - v0.31pre3
Added scale adjustment.
28 Oct 2007 - v0.31
Finalized features in 0.31-preX.
20 Nov 2007 - v0.32
Added functionality for histograms to avoid joining neighbouring bins if their spans are not abutting.
Added ability to define rules based on format characteristics of data (e.g. color, thickness).
Added "restart" flow control for rules.
Fixed image output for Windows users.
3 Dec 2007 - v0.33
Adjusted ideogram spacing to allow pair-wise spacing definitions based on tag.
Fixed axis break issue when a break value was required but break parameter was not set.
Added text labels on ticks.
22 Dec 2007 - v0.34
Rewrote label snuggling method.
Added ability to turn text tracks into glyph tracks.
Fixed rule condition evaluation to allow broader range of characters.
24 Dec 2007 - v0.35
Unit-related error messages now more explicit.
Various fixes for handling bezier_radius.
3 Jan 2008 - v0.36
Imagemap output reformatted and made consistent.
27 Feb 2008 - v0.37
Added ability to set image background to transparent or a custom image.
Adjusted color allocation to avoid duplicate allocation of identical colors.
9 Apr 2008 v0.38
Added support for stacked histograms and ability to independently set radius for each link end.
Fixed histogram fill to drop to y=0 (or closest) level.
Circos now requires Clone module (http://search.cpan.org/~rdf/Clone-0.28/Clone.pm)
14 Apr 2008 v0.39
Added ability to orient ideograms and scale in a counterclockwise orientation using angle_orientation parameter.
Adjusted the way joined histogram bin stroke is drawn.
Fixed bug in which joined histograms bins were not being filled in correctly.
Fixed bug with text offsets at 12 o'clock position.
21 Apr 2008 v0.40
Added SVG output support.
23 Apr 2008 v0.41
Fixed bug which caused incorrect plot scaling when min>0.
Fixed a svg bug which caused images with single unspaced ideograms to display incorrectly.
Adjusted svg-related coded to avoid PNG color palette limitations (you can now have more than 256 colors in color.conf when using svg).
Modified SVG Bezier curves to use crest parameter.
28 Apr 2008 v0.42
Fixed a bug which prevented ribbons from displaying in svg files.
12 May 2008 v0.43
Tick labels can be made relative to ideogram length using relative_label.
Tick spacing can be made relative using rspacing/spacing_type.
Individual ideograms can be placed at different radius.
There is now an installation script which adjusts the Perl binary location and tutorial file output directory.
18 Jun 2008 v0.44
Fixed bug that prevented scientific notation with capital E from being parsed correctly.
Fixed bug that prevened tick mark labels from being rounded correctly.
Default ideogram spacing value can be set to be relative to total size of ideograms.
The parameter chromosomes_units can be set relative to total size of ideograms.
Added skip_run and min_value_change options to plots
The "-" character can be again used in ideogram names
PNG and SVG files can now be created at the same time
25 Jun 2008 v0.45
A variety of speed optimizations were done.
- GD brush initialization
- added memoization to speed up certain function calls
- reduced debug reporting overhead
Overall speed improvement is about 3- to 4-fold for core functions.
23 July 2008 v0.46
Fixed ideogram lookup bug when display order was customized.
Added a variety of helper scripts to create and filter data and to order chromosomes (see tools/)
Added 24-bit PNG support and adjusted color allocation accordingly
30 Sep 2008 v0.47
IMPORTANT: Math::BigFloat is now required.
Added error trap if old version of GD is used that does not support 24bit flag.
Added support for alpha channel in PNG images - now colors can have transparency level.
Fixed brush bug for outlined ribbons with newer GD version.
Added -show_ticks as a command-line parameter (to unset use -no-show-ticks).
Added -show_tick_labels as a command-line parameter (to unset use -no-show-tick_labels).
Added -silent for completely quiet operation (nothing reported to STDOUT).
Improved tick suppression consistency when tick_separation was defined.
Precision in tick mark formatting is improved with Math::BigFloat (this module is now needed).
Added ticks for specific positions via "position" and "rposition" parameter.
Added connector track (currently experimental). This will be documented in an upcoming release.
21 Oct 2008 v0.48
Direction of individual ideograms can be reversed with chromosomes_reverse.
Twist of ribbons is now correct, with a ribbon linking the start and end coordinates of each span.
Ribbon twists can be forced with twist=1 or removed with flat=1.
Individual link coordinates can be inverted by using start>end or inverted=1 parameter.
Added plot of type=highlight to allow highlights to be drawn at any z-depth.
Finalized connector track.
Added band_transparency to allow drawing semi-transparent cytogenetic bands on top of ideograms.
30 Jan 2009 v0.49
Optimized calls to Math::Bezier to reduce time taken to draw links.
Inverted link coordinates (i.e. end<start) can be tested with _REV1_ and _REV2_ in rules.
Fixed error that caused ends of ribbons to be drawn as straight lines.
Fixed error that caused highlights to be drawn on top of the grid in certain cases.
26 Jun 2009 v0.50
Added file_delim to allow any field delimiter to be used in input files (e.g. a tab).
Added sanity check for True Type font support in GD.
Added antialiasing to lines and polygins. Limitations in gd prevent antialiasing of lines that have a thickness >1 pixel or that use a color with an alpha channel.
Fixed bug with parameter parsing that was using = as a delimiter.
Added image maps (via the url parameter) to ideograms, bands, ticks, highlights, tiles, ribbons, text, scatter plots, histograms and heat maps. This is described in Tutorial 10.
Backend implementation has been adjusted, with Circos code moved to Circos.pm module (credit goes to Ken Youens-Clark (CSHL)).
5 Jul 2009 v0.51
Added more comprehensive options to show and suppress tick marks based on ideogram and position.
Fixed scale zooming for display at base resolution.
Expanded and streamlined tick mark functionality.
24 Nov 2009 v0.52
A bug release that fixes issues with ordering and axis breaks.
Ideogram labels can now be rendered with their baseline parallel to the circle's circumference by using label_parallel=yes in the <ideogram> block.