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)

Changes in version 1.13.3 (2024-10-04)
+ plotPatterns for pretty plotting

Changes in version 1.13.4 (2024-10-10)
+ VariantAnnotation moved to Suggests

Changes in version 1.15.1 (2024-11-16)
+ can override alignment endness when loading BAM

Changes in version 1.15.3 (2025-03-05)
+ test coverage for namespaces
+ new ref

Changes in version 1.19.1 (2026-01-02)
+ API change for thresholding in all 'generate*Report' functions
+ filtered out reads are dropped and not counted as hypomethylated anymore

Changes in version 1.19.2 (2026-01-19)
+ limit/clip reads to targets during BAM loading
+ filtering by number of context sites
+ new defaults for filtering

Changes in version 1.19.3 (2026-01-25)
+ checks conventional base probabilities in long-read data
+ accuracy comparison vs modkit
