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

Release v0.6.4

• Adds a function (choose_tx) to select a subset of transcripts per junction that are more likely to be affected by a junction.
• Removal of the column "AS_event_ID" from the RNA junction output
• exon_in_intron() now expects a data.frame

Release v0.6.3

• parse_pangolin and format_pangolin support Pangolin decrease scores (negative scores)
• parse_pangolin is generalized to to Pangolin output generated with optional Pangolin parameter -s
• parse_pangolinworks for vcfs with only one variant
• spliceai_output.pangolin.vcf is updated
• annotate_mut_junc should remove predicted effects outside of transcript range
• add_peptide returns full protein sequence until first stop codon