This is a major version change due to reorganisation of the package structure, obtained by merging
the defunct pymisc-utils (see [pyllars](https://github.com/bmmalone/pyllars)) and [riboseq-utils](https://github.com/dieterich-lab/riboseq-utils).
The package name has been changed from `bio_utils` to `pbio` to reflect this change in API.
Changed
- Changed `star_utils` to `pgrm_utils` and add functions for cmd parser to call flexbar
- Rename ORF files in `ribo.ribo_filenames`, adjust ORF labels in `ribo.ribo_utils`
- Configure setup() using setup.cfg
Fixed
- Missing parameters in function calls, hard coded defaults
- Missing argument for BED6 in `bed_utils.get_all_bed_sequences`.
- Call to `shell_utils` in `bam_to_wiggle.py`.
Added
- New file for ORF labels in `ribo.ribo_filenames`
- Add backend option to `parallel`, enabling to resort to the old `multiprocessing` backend.
- Various functionality to `bam_utils` to filter BAM files by tag, flag;
rewrite `remove_multimapping_reads` into `remove_multimappers`, the former
to be deprecated.
- Added to bio_programs `create_init_ribo_track.py`.