view release on metacpan or  search on metacpan

Changes  view on Meta::CPAN

     images that are different at the byte level.
	
2.38
   - If left labeling requested and the selected font size is larger than the available height,
     then go to smallest available font (gdTinyFont).

2.37
   - Merge fix for incorrect parsing of feature_file sections (issue #6)
   - Added decorated_transcript glyph
   - Added nathanweeks fix for broken heatmap glyph

2.36
   - Fix regression in glyph parent_feature() method so that it once again returns
     the parent of the current feature.
   - Remove recommended prerequisite of Bio::SCF, which is hardly used now.

2.35
   - Change Glyph/segments.pm to work with both variants of CIGAR strings.	
   - Workaround for broken useFontConfig() support in versions of GD prior to 2.50.
   - Fix "gdTinyFont doesn't support height() method error in xyplot".

2.34 Thu May 16 15:42:25 CDT 2013
    - Fixed silent crashes when rendering with the GD::SVG class.

2.33 Fri Feb 22 15:58:10 EST 2013
    - Add truetype support. Enable by passing -truetype=>1 to Bio::Graphics::Panel->new()

2.32 Mon Dec 10 05:47:45 EST 2012
   - Clean up appearance of crossbox to avoid odd black bar in the middle.

2.32 Mon Dec 10 05:47:45 EST 2012
   - Clean up appearance of crossbox to avoid odd black bar in the middle.

2.31 Tue Sep 25 22:39:43 EDT 2012
   - Fix infinite loop when drawing wiggle_xyplots with z-score scaling
     over regions that do not vary much.

2.30
    - Added the glyph for FlyBase's "stacked wiggle" plot (fb_shmiggle.pm) as well as a utility script for preparing the data (index_cov_files.pl).

2.29
    - Fixes for Bio::Graphics::Wiggle to prevent crash when the "bottom" keystyle selected.
    - Add ability to obtain Bio::Graphics::Wiggle features directly from the 
    Bio::Graphics::Wiggle::Loader without creating an intermediate gff3 file.

2.28
    - Fixes to restore density plot functionality in hybrid_plot and vista_plot.
    - Fix handling of Bio::Graphics::Wiggle files in xyplots.

2.27
    - Fix handling of code ref subs to allow for option=>\&Packagename::functionname.

2.26
    - Support for normalizing quantitative plots across entire track.
    - Support for transparency within tracks, allowing features to overlap.
    - Support for -color_series and -color_cycle options (see Bio::Graphics::Panel)
      which cycle dynamically among a fixed series of background colors.

2.25
    - Deprecate xyplot "histogram" subtype and default to "boxes".
    - Add xyplot overlay feature.
    - Fix gene glyph so that it collapses appropriately when bump explicitly
      set to 0.
    - Highlighting now works on features contained within groups.

2.24
    - In feature file configuration sections, allow a tag to contain ":".
  
2.23
    - Workaround a problem in BioPerl 1.069 which prevents FeatureFile from rendering
      properly. Fixed in 1.06902 and higher.
    - Fix issue which caused the track bgcolor property to be ignored in some cases.

2.22
     - Changed package "Math" to "Bio::Graphics::Math" to avoid CPAN namespace
       collisions.

2.21
     - Changed almost all occurrences of attributes() into eval{$feature->get_tag_values()}
       to achieve compatibility with Bio::SeqFeatureI. One exception is in spectrogram glyph,
       which depends on the non-standard behavior of attributes() when called with no args.
 
2.20
     - Fixed the various "wiggle" glyphs so that scale is always drawn even if no data is to be
       shown in selected region.

2.19
     - Made "record_label_positions" default to "true" for wiggle_density plot. This activates
       a fixed-position floating label when density plots are being shown in GBrowse.
     - Fixed a bug in wiggle_xyplot that prevented plot from being drawn in SVG renderings.

2.18
     - Made handling of min/max scale calculations consistent across all xyplot glyphs and their derivatives.
     - Added following autoscale options to wiggle_xyplot and wiggle_whiskers: "z-score" to rescale data such
       that mean is zero and values are standard deviation-fold change; and "clipped_global" to scale to
       global mean +/- some number of standard deviations indicated by "z_score_bounds".
     - Added "z_score_bounds" option to wiggle_xyplot and wiggle_whiskers to control how many standard
       deviations to show.
       

2.17
     - In segments glyph, fixed bleedover of "deletion" color when a deletion is followed by an insertion.
     - In segments glyph, fixed the display of inserted bases such that they will not bleed into a
       preceding deletion.
     - In segments glyph, fixed the mismatch color highlighting when the alignment is to the negative
       strand.
     - In segments glyph, fixed the default colors for mismatch, insertion and deletion.
     - In segments glyph, fixed treatment of soft clipping as an "insertion"; this will avoid the insertion
       color from appearing at the ends of soft-clipped reads.
     - In gene glyph, fixed occasional linking of two neighboring transcripts.
     
2.16
     - Distinguish between "chromosome" and "global" autoscaling in the xyplot and density glyphs.
       Global autoscaling only works when underlying database is bigwig.
     - Regularized options which select glyph subtypes with an option named "glyph_subtype".

2.15
     - Fixed documentation bug: sort_order options to sort by feature length should be
       "longest" and "shortest" rather than "longer and "shorter".
     - Improved layout algorithm, achieving speedup of ~4x on busy tracks.
     - Fixed font color problems when displaying multiple alignments at DNA level in