Version History and Changes

Version 0.12.0 (2020-11-25)

gff_annotation_extractor: fix bug with -t/--type option which previous didn't do anything (PR #49)
gff_annotation_extractor: fix bug when annotating non-htseq-count feature files which didn't have a header (PR #48)
gff_annotation_extractor: update the documentation to clarify function and usage (PR #47)

Version 0.11.0 (2020-09-02)

Updated licence to Academic Free Licence 3
Standardise the utility names to gff_annotation_extractor, gff_cleaner and gtf_extract (NB the old names are still available but will be dropped in a future release) (PR #41)
Updated to support Python 3 (versions 3.5, 3.6, 3.7 and 3.8); Python 2.7 is still supported but will be dropped in a future release (PR #34)
gtf2bed: new option -o allows output file to be specified (PR #28)

Version 0.10.3 (2019-09-10)

Bugfix patch release.

GFFcleaner: fix bug with --clean option when GFF attributes don't include SGD values (PR #12)

Version 0.10.2 (2019-09-09)

Bugfix patch release.

GFFcleaner:: fix bug with --clean-score option when GFF has score values which are not blank, don't start with Anc_, or are non-zero (PR #11)

Version 0.10.1 (2019-02-11)

Patch release to update installation documentation (no other functional changes or bug fixes)

Version 0.10.0 (2018-10-04)

General:

Documentation updated to indicate that only Python 2 is supported; setup.py also includes python_requires keyword which is valid for pip >= 9.

GTF_extract:

Fix the broken -o option.
New option -k/--keep-header will copy the header of the input file to the output.