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 Changes in version 1.1.0 (2021-05-21) + released at bioconductor Changes in version 1.1.9 (2021-09-19) + very fast end memory-efficient BAM loading using HTSlib - for now reads paired-end BAM only + min.baseq to reduce the effect of sequencing errors + very fast Fisher Exact from HTSlib + old code removed Changes in version 1.3.2 (2021-12-24) + more efficient data handling (XPtr instead of Rcpp::wrap'ping) Changes in version 1.3.6 (2022-02-16) + significant speed-up (1.3.5) + methylation patterns Changes in version 1.9.2 (2023-06-21) + both paired-end and single-end alignments Changes in version 1.9.4 (2023-07-03) + methylation calls for bwa-meth, etc Changes in version 1.9.8 (2023-09-29) + creates sample BAMs + linearized MHL Changes in version 1.11.4 (2024-02-11) + methylation calls for bsmap Changes in version 1.11.5 (2024-02-12) + RRBS-ready Changes in version 1.11.6 (2024-02-29) + float and array tags in simulateBam + long-read data input (not optimised yet) Changes in version 1.11.7 (2024-03-05) + optimised reporting from long-read data Changes in version 1.11.8 (2024-03-12) + stricter filtering in lMHL reports Changes in version 1.11.9 (2024-03-21) + uses less memory (due to packed SEQ and XM)