New Features
- `fold`, `graph roc`, and `graph aucroll` now allow specifying sections independently from those used for `mask`, making it easier and less confusing to use structure prediction. Also, they accept a new `--fold-full/--fold-table` option to control whether they use the full reference (default) or the section from the table, if no sections were explicitly specified.
- `mask` now allows choosing whether to drop (default) or keep paired-end reads with discontiguous mates (although discontiguous mates are still incompatible with observer bias correction).
- `cluster` now accepts masked datasets that have been processed with `join` in addition to straight from `mask`.
Performance Enhancements
- Observer bias correction now offers a quick approximate algorithm that typically scales linearly (rather than cubicly) with the sequence length, which greatly speeds up `cluster` and `table`, especially for long sequences. The original algorithm is still available with the flag `--exact-unbias`.
- Calculating coverage during the `mask` and `table` steps uses a new algorithm that runs faster and requires less memory.
- Many options and report fields have been retitled to hopefully make them more self-explanatory.
- Error messages now include the full traceback in double verbose mode (`-vv`), otherwise just the error message itself.
Bug Fixes
- Previously, `join` would ignore section boundaries, yielding incorrect results if the sections overlapped. This issue has been fixed, and join now behaves correctly for overlapping and non-overlapping sections.
- `wf` now generates ROC and rolling AUC plots for the same sections that were folded, rather than looking for the wrong (possibly nonexistant) sections if the sections were not explicitly specified.
- Subprocesses now use the same logging configuration as the parent process, rather than using the default Python logging configuration.
What's Changed
* 0.16.0 by matthewfallan in https://github.com/rouskinlab/seismic-rna/pull/15
**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.15.6...v0.16.0