Changes in version 1.2.1 (2026-03-13)                  

  - Bug fixed: elements and sites with coordinates below 2 or beyond the
    chromosome end now return an informative error, preventing
    downstream failures in trinucleotide context calculations.
  - Bug fixed: all GenomicRanges operations (findOverlaps, setdiff,
    intersect, union) now use ignore.strand = TRUE, ensuring mutations,
    elements, and sites are always matched by genomic position
    regardless of strand.

                 Changes in version 1.2.0 (2022-09-03)                  

  - Updated trinucleotide quantification in sequence and mutations.
    Trinucleotides on the inverse strand are now reverse complemented
    instead of complemented to match COSMIC signatures.
  - More accurate and stable numeric estimates of expected mutations are
    provided as output instead of the Poisson-sampled estimates provided
    previously.
  - The package now allows identification of genomic elements with
    significantly fewer mutations than expected, potentially reflecting
    negative selection of elements. This is enabled using an optional
    command line parameter detect_depleted_mutations. In the analysis
    depleted mutations, elements with enriched mutations are assigned
    non-significant P-values.

                 Changes in version 1.1.2 (2021-11-30)                  

  - Bug fixed: datasets with very few unmutated elements (<10)
    previously failed to include these elements in results.
  - New option: mitochondrial mutations can be analyzed (chrM).

                 Changes in version 1.1.1 (2020-09-17)                  

  - Bug fixed: a rare set of very large elements with depletion of
    mutations would sometimes appear as enriched in mutations.

                 Changes in version 1.1.0 (2020-09-07)                  

Major Changes

  - Alternative reference genomes for human (hg19, hg38) and mouse (mm9,
    mm10) are now supported. Default option is hg19.
  - Full rewrite of ADWGS_rest for memory and speed efficiency.
  - Improved handling on indels on boundaries of elements is now
    default. Removed parameter element_bias that controlled this
    behaviour earlier.
  - README.rd and front page now include a simple example of running
    ActiveDriverWGS, and the vignette has been updated.
  - Site IDs need to match element IDs. Example databases with PTM sites
    have been updated.