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SplAdder version 3.0.0
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@akahles akahles released this 05 Jan 17:00
· 36 commits to master since this release
v3.0.0
bbf2860

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)
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