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)