Changes in version 1.3.5                        

  - Date: 2026-04-23
  - Added the Fisher tests for the odds-ratios. Tests for the
    over-representation
  - Fixed bug in a full pipeline run: possible crash where no duplicated
    reads are present in the input.
  - Computation of hybrids now returns the relative start and end
    coordinates of the dot-bracket string

                        Changes in version 1.3.4                        

  - Date: 2025-09-29
  - Added experimental functionality for prioritisation of ambiguous
    annotation to annotateGi()

                        Changes in version 1.3.1                        

  - Date: 2025-07-04
  - Added trimming of the PE alignments relative to the ligation point.
      - For the PE reads processed by STAR, the type of the junction is
        detected.
      - To narrow down the hybrid prediction, user can trim reads -
        N_trim nt will be left adjacent to the ligation point.
  - Added missing arguments to the function runDuplexDiscoverer which
    runs the whole pipeline. Keys for annotation features, trimming and
    minimum chimeric length cutoffs have defaults, also can be set by
    user to be passed to the functions called from inside the
    runDuplexDiscoverer.

                        Changes in version 1.1.2                        

  - Date: 2025-03-12
  - Removed BiocCheck files

                        Changes in version 1.1.1                        

  - Date: 2024-12-30
  - Added added raw abundance values and duplex counts for 2x2
    contingency table to the p-value calculation output

                       Changes in version 0.99.1                        

  - Date: 2024-10-11
  - Modifications according to Bioconductor - review requirements
  - Fixed bugs in deduplication function
  - Changed splice junction detection getSpliceJunctionChimeras() to
    account for alt 3' and 5' ends

                       Changes in version 0.99.0                        

  - Date: 2024-06-09
  - Submission to Bioconductor