NEWS

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pepitope 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()

pepitope 0.3.3

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

pepitope 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

pepitope 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

pepitope 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

pepitope 0.2.0

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

pepitope 0.1.0

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