3.2ΒΆ
This is a major release with a lot of new features but also some deprecations in preparation for a new 4.0 release.
During the years we have introduced several ways to enable/disable settings. We have used on/off, yes/no, 0/1, true/false. From now on we recommend to only use true/false so that we can unify our config files and make it more intuitive for all pgt-users.
We also removed all 2/3/4 words items and concatenate them now by _
#132.
For example line width
is now line_width
. Thanks @LeilyR!
A few new features in this release:
Every config is now checked for syntax errors before anything is executed (@lldelisle)
Added the possibility to merge transcripts into one single gene representation when using gtf (@lldelisle)
Added the possibility to rasterize bedgraph plots (@lldelisle)
Added the possibility to use summary functions on bedgraphs (@lldelisle)
Generate an empty track if a requested region is not in the given track-files. Fixed #120 (@LeilyR)
Generate an empty track if a chromosome is missing in bedgraph files (@lldelisle)
Improved UCSC style for intron arrows (@lldelisle)
Flybase style now supports color_utr and height_uts (@lldelisle)
A new tracktype
hlines
was added (@lldelisle)Allow to plot the arcs of the links with a color scale based on scores as proposed in #30 (@lldelisle)
Allow to plot rectangle on a heatmap for loops. Fixed #47 (@Phlya, @lldelisle)
A lot of HiC Matrix improvements (@lldelisle)
The
alpha
property can now be used nearly everywhere (@lldelisle)
Also checkout our updated readme).
Special thanks to @lldelisle & @LeilyR for such a feature-rich release.
Merry Xmas and a happy new year! Your PGT team!