Performance Enhancements
- `seismic fold` can now predict secondary structures using multiple threads with the RNAstructure command `Fold-smp` (instead of just `Fold`), which speeds up structure prediction almost linearly with respect to the number of threads. `Fold-smp` is used by default unless the maximum number of processes allowed for folding is 1, in which case `Fold` is used. See https://rna.urmc.rochester.edu/Text/Fold.html for documentation on `Fold` and `Fold-smp`.
Bug Fixes
- Some incompatibilities with prior versions in report field names have been fixed.
- In v0.15.0, the observer bias correction would crash if any position had 0 probability of being covered by a read (i.e. all end coordinate probabilities spanning that position were 0), causing division by zero resulting in NaN values propagating to the objective function. This problem has been fixed by setting the NaN values to 0.
- A new function has been implemented to avoid multiplying invalid values (and generating warnings about doing so).
- In EM clustering, the likelihood should theoretically never decrease between iterations. If it does, then it's either due to a bug in the algorithm or to the accumulation of rounding errors during floating-point arithmetic. In all prior versions, if the likelihood decreased, the algorithm would issue a warning and continue iterating until the likelihood increased by a positive amount less than the threshold. However, this could cause the likelihood to decrease for several consecutive iterations, yielding a sub-optimal solution. In this version, EM clustering will terminate the first time the likelihood increases by less than the positive threshold, including if it decreases.
- In all prior versions,`samtools sort` would use its own default choice for where to write temporary files produced during sorting. In this version, it uses an appropriate sub-directory within the user-specified temporary directory (with `--temp-dir`).
What's Changed
* 0.15.1 by matthewfallan in https://github.com/rouskinlab/seismic-rna/pull/13
**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.15.0...v0.15.1