Seismic-rna

New Features

- Output graphs in SVG and PNG format in addition to CSV, HTML, and PDF.

Performance Enhancements

- `--quick-unbias` now ignores stretches of positions with below-threshold mutation rates, which can cause large speedups on samples with very low mutation rates (e.g. DMS-untreated samples).

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.16.0...v0.16.1

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

Bug Fixes

- Corrected an error preventing masked positions in a table from being inferred.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.15.5...v0.15.6

Command Line

- The observer bias correction now runs by default: `--min-mut-gap` now defaults to 3 rather than 0.

New Features

- Requirement for read weights to sum to a positive real number has been relaxed to a non-negative number.

Bug Fixes

- Removed an incorrect warning message about invalid division during the table step.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.15.4...v0.15.5

New options

- Added option --overhangs/--no-overhangs to control the related portion of mate pairs. --no-overhangs restricts related base calls to those which fall between the start of each mate.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.15.3...v0.15.4

Bug Fixes

- Fixed bug in cluster frequency table where numbers of reads would be normalized to all clusters from all orders instead of within each order.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.15.2...v0.15.3