Seismic-rna

Bug fixes

- Patched bug where `--include-gu` would make SEISMIC-RNA crash. Credit to justinaruda.

Documentation

- Add Justin Aruda (justinaruda) to list of authors.

What's Changed
* 0.9.6 by matthewfallan in https://github.com/rouskinlab/seismic-rna/pull/8


**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.9.6...v0.9.7

Features
- New option `--all-pos/unmasked-pos` in `seismic export web` enables toggling between exporting only unmasked positions (default, and the only option in v0.9.5) and all positions.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.9.5...v0.9.6

Performance
- The function `apply_mask` has been made more efficient in the common case that most of the reads are kept. Credit to justinaruda.

Documentation
- Documentation for the main workflow has been updated.

What's Changed
* Optimized masking by replacing np.intersect1d() with np.setdiff1d(). by justinaruda in https://github.com/rouskinlab/seismic-rna/pull/5
* Improved np.setdiff1d() logic during masking. by justinaruda in https://github.com/rouskinlab/seismic-rna/pull/6
* 0.9.5 by matthewfallan in https://github.com/rouskinlab/seismic-rna/pull/7


**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.9.4...v0.9.5

Bugfixes

- Prior to this release, on some but not all platforms, running multiple EM clustering runs in parallel (but not in series) would cause them to have identical trajectories. I suspect (but have not demonstrated) that this bug happened because on such platforms, the entire Python state (including the random number generator) was copied to each subprocess by `concurrent.futures.ProcessPoolExecutor`. Further suggesting this mechanism, on the same platforms, subprocesses also log messages the same way as the main process, suggesting that the root logger is also copied. So that each clustering run has a unique trajectory even with the same Python state, each clustering run now accepts a seed for its random number generator, which is randomized by the main process to ensure that each clustering run is seeded uniquely.

Internals

- Adopt the convention where all strings use double quotation marks.
- Add more detailed `__str__` methods to some custom classes.

Documentation

- Add more information to the documentation, especially to Manuals -> Workflow.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.9.3...v0.9.4

New Features
- Export mutational and structural data and metadata for the web app using `seismic export web [-S sample-metadata.csv] [-R reference-metadata.csv] [samples ...]`

Bugfixes
- BAM/CRAM files with insufficient reads are no longer returned in the list of output files from the `align` step.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.9.2...v0.9.3

Bugfixes
- Serious memory leaks caused by cached instance methods of the `MutsBatch` class (since v0.9.0) have been fixed (credit to justinaruda).

Internals
- A new `Header` class has been introduced to handle parsing and formatting table headers for types of relationships and/or clusters, along with a test suite for it.
- Both branches for demultiplexing (credit to heWhosShouldersBlockTheSun) have been merged into the main branch.

What's Changed
* Patched several memory leaks in the mask module. by justinaruda in https://github.com/rouskinlab/seismic-rna/pull/2
* Demulti reset by matthewfallan in https://github.com/rouskinlab/seismic-rna/pull/3
* Demult fixed by matthewfallan in https://github.com/rouskinlab/seismic-rna/pull/4

New Contributors
* justinaruda made their first contribution in https://github.com/rouskinlab/seismic-rna/pull/2
* matthewfallan made their first contribution in https://github.com/rouskinlab/seismic-rna/pull/3

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.9.1...v0.9.2