Pygenometracks

Improved documentation:

- fix url of test_data thanks to sonnynguyen
- Better documentation for pyGenomeTracks / makeTracksFile
- Documentation of each track

Enhancements:

- Different bed files format (BED3, BED4, BED5, BED6, BED8, BED9, BED12) is guessed based on the first line and rely not only on number of columns but on the type of each column (string/float etc.). This way, broadPeaks/gappedPeaks and other bed-like formats can be accepted as `file_type = bed` without preprocessing.
- gtf has now its own `file_type`. **Warning**:`file_type = bed` for gtf will be no longer supported in a future version.
- You can use a decreasing x-axis (from larger coordinates to smaller coordinates) with the option `--decreasingXAxis` in `pyGenomeTracks`.
- For bedgraph and bigwig:
- logScale: To apply a log transformation to your data you can set `transform` to `log1p`, `log`, `log2`, `log10`, `-log`. For others than `log1p`, you can set a `log_pseudocount`. By default the y axis values will represent the transformed values and the transformation will be written on the left of the y axis but you can decide to keep the original values by setting `y_axis_values = original`.
- operation on files: You can plot the result of an operation on one or two files without preprocessing. To use it, put the operation in `operation` with the variable `file` or both variables `file` and `second_file`, for example `operation = 0.89 * file` or `operation = max(file, second_file)` or `operation = file - second_file`. In the two later cases, you need to put the path of the second file in `second_file`. However, this operation can be time consuming if you do it multiple times and you may prefer to convert your files in advance.
For more examples on these two new features, visit [the examples](https://pygenometracks.readthedocs.io/en/latest/content/examples.html#log-transform-and-operation-examples)
- Both `type = line` and `type = lines` are working in bedgraph_matrix

Bugfix:

- In version 3.3, if you were using a colormap in bed the `border_color` and `color_utr` were ignored. Now each one can be set to different color/colormap/bed_rgb.

- a documentation on readthedocs: https://pygenometracks.readthedocs.io
- progress bar for bed, gtf, bedgraph, narrowPeak, epilogos
- all colors can be set as `(r, g, b)` with r, g, b values between 0 and 1.
- all colormap can be set as an array of colors, for example `[red, white, (0, 0, 0.5)]`
- the titles on the right can be align left, right or center with the argument `--trackLabelHAlign`
- for the links track,
- `compact_arcs_level` to be able to see both very long arcs and very small arcs.
- `ylim` to be able to zoom and see small arcs.
- a new track type: `file_type = scalebar` which by default is close to the UCSC scale bar.
- for the bed tracks:
- a new gene type: `tssarrow`
- `border_color` and `color_utr` can be set to `bed_rgb`.
- `all_labels_inside` allow to put the name of the region on the left if it ends after the plotted region.
- `labels_in_margin` allow to put the name of the region in the margin if it ends after the plotted region.
- `line_width` can now be set in the narrowPeak tracks.
- `colormap` can now be set in bedgraphMatrix tracks.

bug fixes:
- if a bed with no interval is provided, pgt no longer exit.
- When an exon had both UTR start and UTR end within it, only the UTR start was considered.
- alpha in links tracks was not used
- qcat files with missing values are now working.

- Small bug fix in parser when the parameter had spaces in the name and was a boolean (for example show data range instead of show_data_range).
**Warning:** In version 4.0 no parameter with space will be accepted.

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 `_` (https://github.com/deeptools/pyGenomeTracks/pull/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 https://github.com/deeptools/pyGenomeTracks/issues/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 https://github.com/deeptools/pyGenomeTracks/issues/30 (lldelisle)
* Allow to plot rectangle on a heatmap for loops. Fixed https://github.com/deeptools/pyGenomeTracks/issues/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](https://github.com/deeptools/pyGenomeTracks/blob/master/README.md).

Special thanks to lldelisle & LeilyR for such a feature-rich release.

Merry Xmas and a happy new year!
Your PGT team!

* change infos to warnings (https://github.com/deeptools/pyGenomeTracks/pull/100)

* small bug fix for summit usage (lldelisle)
* I added a vertical bar in the narrowPeaks when plotted as box to be able to see the summits (lldelisle)