# Version  0.99.0 
- Date: 2024-06-09
- Submission to Bioconductor

# 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

# 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

# Version  1.1.2
- Date: 2025-03-12
- Removed BiocCheck files 

# 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`.

# Version  1.3.4
- Date: 2025-09-29
- Added experimental functionality for prioritisation of ambiguous annotation 
  to `annotateGi()` 

# 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
