Changes in version 0.2.1 (2020-12-21) + made this second iteration of epialleleR a usable package Changes in version 0.3.1 (2020-01-01) + heavy refactoring, many internal methods added + C++ functions for nearly all bottlenecks (pending fast: cigar, summary, genome loading) Changes in version 0.3.2 (2021-01-06) + first attempt to stablilize API (generateCytosineReport and generateBedReport) + temporary method for ECDF (generateBedEcdf) + uploaded to GitHub Changes in version 0.3.5 (2021-01-09) + lots of refactoring + new method: preprocessBam() to save time on loading/preprocessing + new C++ sub for CX report with std::map summary (5-10x speedup) Changes in version 0.3.7 (2021-01-12) + lots of refactoring again + CX report sub now uses boost::container::flat_map (additional 2x speedup) + removed dplyr as a dependence, whole package uses data.table now Changes in version 0.3.9 (2021-01-19) + fast C++ CIGAR parser to lay queries in reference space + new method to extract base frequences: generateBaseFreqReport Changes in version 0.4.0 (2021-03-08) + going public + CX report now includes only the context present in more than 50% of the reads + generateVcfReport (capable of dealing with SNVs only for now) + added documentation to some of the methods + added several examples + added sample data for amplicon and capture NGS + added some tests based on sample data + README.md Changes in version 0.99.0 (2021-04-09) + R>=4.0 for submission + removed unused dependencies + correct work of generateVcfReport (although SNV only) + unmatched reads are at the end of generateBed* output now + compiles and works on Apple Silicon (native ARM64 R) + fully documented methods + fully covered with tests and examples + comprehensive vignettes