Changes in version 1.7.1                        

NEW FEATURES

  - Added a long-read processing example in a new vignette.

IMPROVEMENTS

  - Refined recurrent annotation in markRecurrentRegions(). Recurrent
    status is now determined using a minimum overlap fraction between
    events and recurrent regions, preventing marginal overlaps from
    being annotated as recurrent.

  - More precise recurrent region definition in
    identifyRecurrentRegions(). Replaced direct interval merging with an
    overlap-aware, chromosome-wise agglomerative hierarchical clustering
    approach. Recurrent regions are now defined based on overlap
    similarity between events, with configurable clustering stringency.

BUG FIXES

  - Corrected collapsed event size calculation in collapseEvents(). The
    total size of collapsed events is now computed as the true genomic
    span of the region rather than the sum of individual event sizes.

                        Changes in version 1.5.2                        

  - Fix vignette for LatEX error.

                        Changes in version 1.5.1                        

  - Update vignette

                        Changes in version 1.5.0                        

  - Added parallelization option BPPARAM in calculateEvents() and some
    new columns in the output.
  - Added new vignette: "Preprocessing Guide".
  - Update User Guide vignette
  - Add 3 new functions markRecurentRegions(),
    identifyRecurrentRegions() and collapseEvents()

                       Changes in version 0.99.4                        

Final corrections and final editing of vignette

                       Changes in version 0.99.3                        

2nd correction of reviewer's suggestions

                       Changes in version 0.99.2                        

Correction of reviewer's suggestions

                       Changes in version 0.99.1                        

First pre-review corrections

                       Changes in version 0.99.0                        

First release of UPDhmm package