Spladder

This is a bugfix release. It addresses the following issues:

- code was not working with newer version of Matplotli (> 3.7) 192
- program failed when a value for `--psi-min-reads` was provided 190
- out of bounds access when at least one chunk needed to be skipped in count / psi hdf5 197
- improvement of documentation addressing 176 180

This is a bugfix release. It addresses the following issues:
* when chosing the `debug` option, the output was malformed and could lead to a crash 174
* unrecognized chromosome/contig names could lead to crashes when the `sparse-bams` option was used 178
* the option to remove short exons caused the program to crash 177

This is a bugfix release, it addresses the following issues:

- event coordinates displayed in the testing results belonged to the wrong event (158)
- labeling of annotated introns was incorrect for alt_3prime events (163)
- automatic plotting of test results was faulty (165)

This is a bugfix release, which addresses the following issues:

* fixing wrong stacking of exons in intron_retention verification that
led to a bug when option --use-anno-support was used
* exons2 for intron_retentions were not consistently 2D
leading to issues in the downstream usage (fixing 152)
* missing import when counting in single mode (fixing 151)

This is a bugfix release, addressing issue 149.

This is a new major release, as it introduces quite many changes, some of which break compatibility with some of the output of 2.4.x. and earlier versions.

Changelog:
* addition of a label to the output showing whether an intron is annotated in the given annotation
* addition of a label to each event indicating whether it contains one or several annotated vs novel introns (carry through annotation flag from input to output (per isoform))
* the naming convention of count features has been changed to be more general, also generalising the order of exons
* the support for pyproc (that was partially able to submit compute jobs to HPC systems) has been removed, instead use of workflow managers like Snakemake or Nextflow is recommended
* instead of only looking at the RNA-Seq evidence, an event can also be validated using the given annotation information (via a new command line switch `--use-anno-support`)
* chunksize of chunked merge is now configurable
* coordinate string computation has been added to event object
* output of test mode has been made more verbose (including coordinates and exon
usage)
* event ID spelling has been made consistent between build and test modes
* the documentation has been extended

Bugfixes:
* fixed a bug in validation code for mutually exclusive exons
* handling of None-type strand values (147)