What's new in 0.20.1

New Features

• The clustering step now calculates a "jackpotting quotient" to measure how much bias there is in the dataset. The calculation is expensive and can be toggled with --jackpot/--no-jackpot.
• The clustering step now outputs the per-run statistics as a CSV file and a graph for every statistic, rather than writing them into the cluster report.
• It also ouputs scatter plots comparing the observed and expected counts for each number of clusters.
• The new command seismic +datapath locates and prints the location of the data path for RNAstructure (assuming it has been installed properly), to which the DATAPATH environment variable should be set.
• The raise_on_error parameter can now be used to make SEISMIC-RNA raise an Exception instead of logging an error message any time logger.error() or logger.critical() is called. This is useful for testing the whole workflow, when errors should cause the test to fail. Only available through the Python API.
• SEISMIC-RNA now has a new logo!

Bug Fixes

• Fixed a bug where clustering would run by default in seismic wf. Now, clustering is enabled with the flag --cluster.
• Fixed a bug causing seismic align and seismic wf to delete BAM files when aligning demultiplexed FASTQ files.
• Assume that the folding energy for RNA structures missing an explicit energy is 0 rather than NaN.
• Added kaleido to list of dependencies to fix a bug about a missing optional dependency for Plotly.
• Fixed a bug where seismic +sim ends could produce out-of-bounds 5' or 3' ends.

Full Changelog: https://github.com/rouskinlab/seismic-rna/compare/v0.20.0...v0.20.1