- Added support for BED files without comma terminator in fields 11 and 12 (@camillaugolini-iit)
- Added --transcript_feature_name argument for gtf2bed (@camillaugolini-iit)
- Better documentation and examples of API methods
- Fixed shadowing of built-in
allfunction by translateChr()
- Added support for strandedness in tx2genome()
- Fixed bug in tx2genome() strand handling
- Improvements to the CLI messages
- Major documentation rewrite
- Added --filterKey option to gtf2bed
- Fixed exception handling in tx2genome
- Corrected off-by-one error in tx2genome
- Added unit tests for tx2genome
- Various documentation fixes
- Added --whichExon option to bed12tobed6
- Fixed a bug in bed12tobed6