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Releases: ratschlab/spladder

SplAdder version 3.1.0

03 Oct 08:57
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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

23 Apr 14:02
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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

07 Feb 14:31
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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

13 Jul 10:41
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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

28 Jan 11:53
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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

19 Jan 20:40
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This is a bugfix release, addressing issue #149.

SplAdder version 3.0.0

05 Jan 17:00
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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

17 Jun 18:23
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bugfix release - correcting use of cram input in sparse mode

SplAdder version 2.4.3

18 Mar 11:12
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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

19 Nov 10:11
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This release has the following changes:

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