v0.6.14

• fix changed dependency package for makeTxDbFromGFF() function
• Require R >= 4.4
• add automated docker building support

v0.6.13

• Fixed bug leading to incorret peptide sequences
• Simplified code of add_peptide() function
• Added function to calculate distances to next canonical splice sites
• Added function to annotate if junction is potentially a JET (Exon-TE chimera)
• Update of Dockerfile
• Fixed lift-over for deletions in junction location

Full Changelog: v0.6.12...v0.6.13

Release v0.6.12

• Add docker container support
• support parsing of junctions with no strand info from STAR output

Release v0.6.11

• fix of liftover function
• improve warnings and add more tests

Release v0.6.10

• update of combine_mut_junc() to accept empty tables as input
• update of format_cispliceai() to optionally keep gene_ids
• add more tests

v0.6.9

Simplification of function annotate_mut_effect()` and ensuring that same column names are returned if output is empty

Release v0.6.8

• Add function liftover_junc_id() to liftOver splice junctions to other
  reference genomes or personalized genomes

Release v0.6.7

Added:

• New functionality:
  • CI-SpliceAI parsing and formatting functions with example data and tests
  • IRFinder parsing and filtering functions with example data and tests
  • StringTie parsing and formatting functions
  • SUPPA2 parsing and formatting functions
  • STAR parsing and formatting functions with example data and tests
  • RegTools parsing and formatting functions with example data and tests
• add test for empty CI-SpliceAI input file
• add more global variables to avoid notes in R CMD check

Changed:

• Update CI/CD pipeline for less verbosity during R pkg installations
• Return single-row data.frame for empty input in annotate_mut_effect()
• include 'number_of_supporting_reads` when parsing SplAdder output
• generalize generate_combined_dataset() to multiple inputs
• Update README with list of supported tools
• add option consider_intron_retention to annotate_mut_effect()
• adjust syntax for dplyr >= 1.1.1
• remove rarely used pkgs from Imports
• simplify code in parse_spliceai_thresh()
• minor spell check fixes and doc updates

Fixed:

• fix warnings due to NA's in CI-SpliceAI parsing function
• fix use of generate_combined_dataset() in vignette

Release v0.6.6

• add vignette with example workflow
• fix parsing of pangolin results
• simplify README

Release v0.6.5

• Fixed bug while parsing VCF files containing only a single variant
• Improved error handling of spladder import