Changes in version 0.4.0                        

  - Added plot_read_structure() to identify and visualize read features
  - Read feature positions and strand are now identified automatically
    by default
  - mut_id is now shared among variants on the same position (#6)
  - Deprecate plot_reads(), rename to plot_read_count()
  - Deprecate plot_distr(), rename to plot_read_distr()
  - Replace fqtk and guide-counter tools with internal one-pass
    count_fastq()

                        Changes in version 0.3.3                        

  - Speed up runtime by caching txdb-derived objects and reusing them

                        Changes in version 0.3.2                        

  - Add a workaround for EnsDb/BSGenome mismatch on UCSC names (#3)
  - Fix a bug where multi-exon dropping could subset incorrectly (#5)
  - Re-introduce filter that CDS width must be equal variant width (#5)
  - Fix error message when sample sheet does not contain required fields
  - Add clearer error messages about seqlevels mismatches in
    annotate_coding() (#11)
  - Barcode counting now uses --exact-match by default

                        Changes in version 0.3.1                        

  - Multi-exon variants are now dropped with a warning (#5)
  - FASTQ demultiplexing is now done in a clean directory (#7)
  - fqtk and guide-counter are now supplied via R packages
  - fqtk and guide-counter now handle spaces in paths correctly (#8)
  - filter_variants will now error if provided more than one sample
    implicitly

                        Changes in version 0.3.0                        

  - Added QC and screen incl. plotting functionality to the package
  - Added command-line wrappers for fqtk demultiplexing and
    guide-counter
  - Provided usage vignettes for Variant calling, QC and Co-culture
    screen

                        Changes in version 0.2.0                        

  - Added support for RNA-based gene fusion using the rnafusion NF-core
    pipeline

                        Changes in version 0.1.0                        

  - Provided simple variant annotation from the sarek NF-core pipeline