ini format #132
Merged
ini format #132
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* added info in the doc of get_scores * integrate the cases when there is no item in the region * updated output of make_tracks_file
* added info in the doc of get_scores * integrate the cases when there is no item in the region * updated output of make_tracks_file * bedgraph inherit the init from GenomeTracks to have self.log
Narrow peak debug ld
4 tasks
bgruening
added a commit
that referenced
this pull request
Dec 7, 2019
deprecations in preperation 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 word items and concatenate them now by `_` (#132). For example `line width` is now `line_width`. Thanks @LeilyR! Features: * 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 chromosom is missing in bedgraph files. Fixed #120 * 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](). Merry Xmas and a happy new year! The PGT team!
Merged
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
changed all 2 words terms into 1 component of words separated by
_