Bio-Graphics
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- 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
the segments glyph.
- Fixed problem of DNA alignment indels disappearing from view when they span entire region.
- Fixed problem of mismatch and indel colors leaking off ends of feature arrows.
2.14
- Fixes to the way that "fast bump" works so that tracks never fast bump.
This fixes problems when using groups to simulate subtracks, and the
groups are of different heights.
- The group glyph will now add the group labels to the list of track keys
stored in the panel and retrieved from the call to $panel->key_boxes().
2.13
- Changed default namespace for callbacks to make them portable across freeze/thaw
cycles.
2.12 Tue Aug 31 10:42:06 EDT 2010
- Created a read_pairs glyph that contains the settings most often used for SAM paired end reads/mate pairs;
this fixes the mate-pairs overlap bug.
- xyplot glyph now obeys "flip" setting.
2.11 Tue Jun 29 15:37:03 EDT 2010
- Cleaned up stylesheet-based rendering of features when the main glyph has a type of
"hat" and subfeatures overlap with each other. This occurred when rendering certain
DAS sources.
2.10 Mon May 24 13:58:26 PDT 2010
- Fixed a long-standing but rarely-seen bug in layout algorithm that
caused some features to be displaced downward further than they should
be.
- Added support for labeling groups (on the left side). This is used by
GBrowse to create subtracks.
2.09 Fri May 14 11:46:51 EDT 2010
- Fixed Bio::Graphics::FeatureFile cached callbacks so that they are evaluated
in the same package as they were when the file was originally evaluated and cached.
2.08 Thu May 13 17:06:29 EDT 2010
- Fixed Bio::Graphics::FeatureFile init_code so that it is reinvoked when retrieving a
cached copy of parsed featurefiles.
2.07 Sun May 9 11:56:10 EDT 2010
- Added FeatureFile->cachedir argument to help with GBrowse tests.
2.06 Wed May 5 00:51:00 EDT 2010
- Segments glyph now displays correct mismatch color for sequences that begin or end with soft clips.
- Indels displayed in correct color when indel begins or ends outside current visible region.
2.05 Identical to 2.04.
2.04 Sun Apr 18 17:26:01 EDT 2010
- Segments glyph now smarter about fetching reference sequence; this improves performance
on multiple alignments.
- -show_mismatch option now takes following arguments: 0 (false), "always", "base level" (draw only
when DNA is in view), or a number, in which case mismatches will only be drawn when the length
of the window is <= that number. For compatibility, a value of "1" is the same as "base level."
- Fixed display of protein sequence in genes when -draw_protein is true.
- Fixed display of long deletions in segments glyph base-pair alignments to avoid drop-out of
sequence from the right end of the alignment following deleted region.
- Fixed display of insertions in segments glyph base-pair alignments so that the length
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