NEWS

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epialleleR 1.11.9 (2024-03-21)

• uses less memory (due to packed SEQ and XM)

epialleleR 1.11.8 (2024-03-12)

• stricter filtering in lMHL reports

epialleleR 1.11.7 (2024-03-05)

• optimised reporting from long-read data

epialleleR 1.11.6 (2024-02-29)

• float and array tags in simulateBam
• long-read data input (not optimised yet)

epialleleR 1.11.5 (2024-02-12)

• RRBS-ready

epialleleR 1.11.4 (2024-02-11)

• methylation calls for bsmap

epialleleR 1.9.8 (2023-09-29)

• creates sample BAMs
• linearized MHL

epialleleR 1.9.4 (2023-07-03)

• methylation calls for bwa-meth, etc

epialleleR 1.9.2 (2023-06-21)

• both paired-end and single-end alignments

epialleleR 1.3.6 (2022-02-16)

• significant speed-up (1.3.5)
• methylation patterns

epialleleR 1.3.2 (2021-12-24)

• more efficient data handling (XPtr instead of Rcpp::wrap'ping)

epialleleR 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

epialleleR 1.1.0 (2021-05-21)

• released at bioconductor

epialleleR 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

epialleleR 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

epialleleR 0.3.9 (2021-01-19)

• fast C++ CIGAR parser to lay queries in reference space
• new method to extract base frequences: generateBaseFreqReport

epialleleR 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

epialleleR 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)

epialleleR 0.3.2 (2021-01-06)

• first attempt to stablilize API (generateCytosineReport and generateBedReport)
• temporary method for ECDF (generateBedEcdf)
• uploaded to GitHub

epialleleR 0.3.1 (2020-01-01)

• heavy refactoring, many internal methods added
• C++ functions for nearly all bottlenecks (pending fast: cigar, summary, genome loading)

epialleleR 0.2.1 (2020-12-21)

• made this second iteration of epialleleR a usable package