NEWS

---

txcutr 1.15.2

NEW FEATURES

• None.

SIGNIFICANT USER-VISIBLE CHANGES

• Removed deprecation notice.
• Updated author email.

BUG FIXES

• Added GenomeInfoDbData to Suggests (Issue #23).

txcutr 1.10.0

NEW FEATURES

• None.

SIGNIFICANT USER-VISIBLE CHANGES

• Updated author email.

BUG FIXES

• None.

txcutr 1.9.1

NEW FEATURES

• None.

SIGNIFICANT USER-VISIBLE CHANGES

• Switched TxDb creation from GenomicFeatures to txdbmaker.

BUG FIXES

• Compatibility with Bioconductor 3.19 (devel).

txcutr 1.0.0

NEW FEATURES

• None.

SIGNIFICANT USER-VISIBLE CHANGES

• Bioconductor 3.14 release

BUG FIXES

• None.

txcutr 0.99.0

NEW FEATURES

• Staged for Bioconductor submission.

SIGNIFICANT USER-VISIBLE CHANGES

• None.

BUG FIXES

• None.

txcutr 0.3.2

NEW FEATURES

• Improved vignette

SIGNIFICANT USER-VISIBLE CHANGES

• None.

BUG FIXES

• None.

txcutr 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.

txcutr 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.

txcutr 0.2.2

NEW FEATURES

• None.

SIGNIFICANT USER-VISIBLE CHANGES

• None.

BUG FIXES

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

txcutr 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.

txcutr 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.