Seismic-rna

Bug fixes

- Since v0.9.0, there has been a bug in merging paired reads (function `merge_rels`) preventing a match in one read from compensating for ambiguity in the other. For instance, if at position 45, read 1 had a low-quality N while read 2 had a high-quality match, then the result would be a low-quality N, instead of the intended high-quality match. This bug did not prevent matches from compensating for blank positions, nor did it prevent non-matches from compensating for other types of relationships. This bug was found by justinaruda and has now been patched by matthewfallan and justinaruda.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.14.0...v0.14.1

New Features

- Introduce command `+listpos` to list positions from table files that meet certain criteria.
- Introduce file format for listing positions.
- In `mask` command, introduce `--exclude-file` which accepts a file containing a list of positions and excludes them; the preceding option `--exclude-pos` has been removed.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.13.1...v0.14.0

Performance

- Graphs now check whether their output files exist before computing their data, which can save a lot of time for expensive graphs (e.g. rolling AUC-ROC).

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.13.0...v0.13.1

New Features

- Join sections (horizontally) from Mask or Cluster reports using new command `seismic join`.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.12.2...v0.13.0

New Features

- The new command `seismic +delclust` deletes clusters of order higher than a maximum you specify.

Removed Features

- For consistency with the other commands (especially with `--force`), `+addclust` and `+delclust` no longer make backups. This feature will probably be reimplemented in a future update that causes all commands to write to a temporary directory first before moving all files to the output directory; but this priority is low, since SEISMIC-RNA has worked well enough without this safety feature.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.12.1...v0.12.2

CLI changes

- `+clustup` has been renamed to `+addclust` to make its purpose more obvious.

New Features

- `+addclust` now makes a temporary backup of every file in a clustering directory before modifying the existing files (batches, counts, and report). If a fatal error occurs while modifying the existing files, then the original files are restored from the backup. Without this feature, the original data could be corrupted and rendered unusable.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.12.0...v0.12.1