Methscan

This release introduces the `--bridge-gaps` parameter to `methscan scan` and `methscan diff`.

By default, `methscan scan` runs a sliding window along the genome. Overlapping windows exceeding a certain variance threshold are then merged in a peak-calling procedure, yielding VMRs of variable size depending on the width of the variance peak. If there are long stretches of variably methylated DNA, this peak-calling can sometimes produce "fragmented VMRs", i.e. many nearby VMRs that are separated by very small gaps:
In this illustration, many VMRs (thick vertical purple lines) were detected in the gene body of the depicted gene. Since some of these VMRs are only separated by a tiny gap, it may be more appropriate to merge them into one continuous, large VMR.

This VMR merging is now possible by setting `--bridge-gaps` to e.g. 1000, which would mean that VMRs with a gap of 1000 bp or less will be merged into one VMR, as illustrated here on some mock data:
(red thick line: regular VMR peak calling; blue thick line: VMR peak calling with `--bridge-gaps 400`. The variance threshold is at 0.55; the y position of the thick lines has no meaning).

The same functionality was also added to the DMR detection approach implemented in `methscan diff`.

This release also fixes a minor bug in the calculation of the adjusted p-values associated with DMRs.

This is a minor release that links our [publication](https://doi.org/10.1038/s41592-024-02347-x) and [website](https://anders-biostat.github.io/MethSCAn/) in the CLI help messages.
Furthermore, MethSCAn now prints an appropriate error message if you provide it with an empty bed file.

This is a minor release that adds three tiny features:

1. `methscan filter` can now filter in place, i.e. overwrite its own input directory with a filtered version of itself
2. `methscan scan` now aborts properly when no VMRs above the `--min-cells` threshold are found
3. Added a command to show citation info and a link to our paper.

This is the initial release of MethSCAn upon acceptance of our paper. The main difference is that we renamed the package from `scbs` to `MethSCAn`.

For earlier releases and changelogs, check the old [repository](https://github.com/LKremer/scbs) and its [release page](https://github.com/LKremer/scbs/releases).