Added
- Added to bio_programs `bed_to_bigBed`, `run_signalp` and `run_tmhmm`.
Removed
- Removed deprecated function calls from bio_programs `parse_meme_names`,
`create_mygene_report`, `get_all_utrs`, `get_read_length_distribution`,
`count_reads` and `count_aligned_reads`.
- Removed deprecated function calls from `bed_utils`.
- Removed deprecated function calls from
`fastx_utils`, `bam_utils`.
- Removed deprecated function call from `gtf_utils`.
Fixed
- Minor changes to `bio_utils.plotting.plot_read_length_distribution`,
see [ISSUE 87](https://github.com/dieterich-lab/rp-bp/issues/87).
Added
- Added _partial support_ for GFF3 specifications, in particular this requires removing the
STOP codons from the CDSs. Reference annotations file with gff extension are now
treated as GGF3.
- Handling of additional options passed to star via arguments to `star_utils`.