Merry Xmas 2019

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!