SplAdder version 3.1.0

This releases fixes several bugs and augments the output for intron retention events

• CIGAR strings containing the characters = or X instead of M have been incorrectly parsed, leading to wrong intron coordinates. Any runs with input files containing such CIGAR strings should be re-run
• The output of intron retention events was lacking the column e2_cov_region as described in the documentation (#199). This has been fixed.
• When using the option --use-anno-support exons were stacked incorrectly, leading to crashes.
• The help screen now shows the SplAdder version (#202)

SplAdder version 3.0.5

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

SplAdder version 3.0.4

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

SplAdder version 3.0.3

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)

SplAdder version 3.0.2

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)

SplAdder version 3.0.1

This is a bugfix release, addressing issue #149.

SplAdder version 3.0.0

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)

SplAdder version 2.4.4

bugfix release - correcting use of cram input in sparse mode

SplAdder version 2.4.3

Bugfix release

• move to numpy and remove deprecation warnings
• address #115 and #122
• address parsing problem when input bam files and have the form *bam.bam

SplAdder version 2.4.2

This release has the following changes:

• improved handling of CRAM input files
• fixing a bug leading to truncated sample names in distributed quantification