Changes in version 0.99.0                        

NEW FEATURES

  - Staged for Bioconductor submission.

SIGNIFICANT USER-VISIBLE CHANGES

  - None.

BUG FIXES

  - None.

                        Changes in version 0.3.2                        

NEW FEATURES

  - Improved vignette

SIGNIFICANT USER-VISIBLE CHANGES

  - None.

BUG FIXES

  - None.

                        Changes in version 0.3.1                        

NEW FEATURES

  - Compressed outputs.
  - Tests for proper handling of transitive merging. Overlaps that merge
    A -> B and B -> C, but not A -> C, will output A -> C and B -> C.
    That is, transitivity is applied and the final output will always
    use the distal most transcript in a chain as the final output.

SIGNIFICANT USER-VISIBLE CHANGES

  - All export*() methods now include automatic detection of .gz
    filenames, which toggles the use of compressed (gzip) exports.

BUG FIXES

  - None.

                        Changes in version 0.3.0                        

NEW FEATURES

  - Merge table generation and exporting.

SIGNIFICANT USER-VISIBLE CHANGES

  - Adds generateMergeTable() and exportMergeTable() for creating a
    merge table for transcripts that are not separated by a thresholded
    distance. Such files can be used by transcript quantification tools
    to specify what transcripts should be merged.

BUG FIXES

  - None.

                        Changes in version 0.2.2                        

NEW FEATURES

  - None.

SIGNIFICANT USER-VISIBLE CHANGES

  - None.

BUG FIXES

  - The BPPARAM was not being passed through to internal bplapply calls.

                        Changes in version 0.2.1                        

NEW FEATURES

  - Added a NEWS.md file to track changes to the package.
  - Provide more control over parallel execution.

SIGNIFICANT USER-VISIBLE CHANGES

  - The truncateTxome() method includes an optional BPPARAM with which
    users can pass a specific BiocParallelParam. If not provided, it
    will respect the result of BiocParallel::bpparam(), which can be
    globally set using BiocParallel::register().

BUG FIXES

  - None.

                        Changes in version 0.2.0                        

NEW FEATURES

  - Adds deduplication behavior. Note that deduplication does not
    exclude transcripts from different genes.

SIGNIFICANT USER-VISIBLE CHANGES

  - The truncateTxome() method now deduplicates transcripts spanning
    identical ranges after truncation.

BUG FIXES

  - None.