Rpbp

Changed

- Example dataset updated and moved to new address. Updated documentation.
- `predict_translated_orfs` and `select_final_prediction_set` modified such
that Rp-chi pipeline is used _only_ if `chi_square_only` is in config file,
otherwise Rp-Bp is used.
- Handling of options passed to flexbar via arguments to `run_all_rpbp_instances`,
`run_rpbp_pipeline`, `create_orf_profiles` and `create_base_genome_profile`.
- Handling of additional options passed to star via arguments, mainly
to `create_base_genome_profile`.

Removed

- Removed config option `seqids_to_keep` for compatibility with `extract_metagene_profiles`
that does not use this option anymore. This has also been removed from the example.
Updated documentation.
- Removed fields `delta_l` and `delta_h` from output in `estimate_orf_bayes_factors`.
- Removed deprecated function calls from
`analysis/profile_construction/get_all_read_filtering_counts`,
`prepare_rpbp_genome`, `create_base_genome_profile`

Added

- Utility for supressing pystan (or other compiled function) output. For more
details see [Issue 10](https://github.com/dieterich-lab/rp-bp/issues/10).
- Added _limited support_ for GFF3 specifications, in particular this requires removing the
STOP codons from the CDSs and passing the right option to `STAR`.
`Prepare_rpbp_genome` and `create_base_genome_profile` modified.
- If using de_novo, all annotations are concatenated automatically in preparation of
running the main pipeline.

Fixed

- Minor changes to plotting options, typos and/or redundant features in
`rpbp/analysis/profile_construction/create_rpbp_preprocessing_report` and
`rpbp/analysis/profile_construction/visualize_metagene_profile_bayes_factor`.
See [ISSUE 87](https://github.com/dieterich-lab/rp-bp/issues/87). In progress.
- Added default _sjdbOverhang_ option to star during mapping.

Removed

- Removed deprecated function calls from `analysis/rpbp_predictions/add_mygene_info_to_orfs`,
`analysis/find_differential_micropeptides`, `analysis/proteomics/get_orf_peptide_matches`
and `analysis/proteomics/filter_nonunique_peptide_matches`

Fixed

- In `create_rpbp_preprocessing_report.create_figures` call to
`filenames.get_riboseq_profiles` modified to fix file name reference issue.
- In `create_rpbp_preprocessing_report` some figures were referenced before they were created,
as a _temporary fix_, the function `create_figures` is now called earlier.
- Minor typos in some of the analysis scripts.

Added

- Flag added to differentiate between _exons_ file (list of exons for any given transcript),
and _orfs_ file (technically, a list of exons per orf).
See [Issue 59](https://github.com/dieterich-lab/rp-bp/issues/59) for more details.

Updated

- Dependencies to new repo locations.

Added

- Reference to helper script to install prerequisite programs. See
[Issue 75](https://github.com/dieterich-lab/rp-bp/issues/75) for more
details.

Updated

- Dependencies to new `pymisc-utils` and `pybio-utils` repos. See
[Issue 74](https://github.com/dieterich-lab/rp-bp/issues/74) for more
details.

- Version specification of prereqs

Removed

- `cluster-subcodon-counts`. See [Issue 78](https://github.com/dieterich-lab/rp-bp/issues/78)
for more details.

Added

- Documentation for using custom alignment files. Please see
[Issue 73](https://github.com/dieterich-lab/rp-bp/issues/73) for more
details.

Fixed

- Documentation links to old ipython notebooks. Please see
[Issue 71](https://github.com/dieterich-lab/rp-bp/issues/71) for more
details.

Fixed

- Incorrect read filtering report. See [Issue 69](https://github.com/dieterich-lab/rp-bp/issues/69)
for more details.

- Broken download link for example.

Fixed

- Incorrect alignment of ORF data frame and profile matrix. See
[Issue 54](https://github.com/dieterich-lab/rp-bp/issues/54) for more details.
- ORF coordinates for start codon on exon boundary. See
[Issue 64](https://github.com/dieterich-lab/rp-bp/issues/64) after the
reopening for more details.