Seismic-rna

New Features

- Enabled simulating data with no two mutations too close (controlled by `--min-mut-gap`).
- Changed behavior of the mutation rate simulator so that each base has the same paired and unpaired mutation rates in every cluster, which is more realistic than the previous behavior of entirely different mutation rates in every cluster.
- Added feature where the Illumina universal adapter (`AGATCGGAAGAGC`) is appended automatically to any insert that is shorter than the read length, to make the simulation mimic Illumina sequencers more realistically.
- Updated the directory structure of the simulation outputs to avoid possible name conflicts.
- Added subcommand `seismic +sim params` to simulate all parameters in one step.
- Added option `--fq-gzip/--fq-text` simulate FASTQ files with or without gzip compression.

Bug Fixes

- Fixed bug in `seismic fold` where a temporary CT file would be written to the output directory.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.17.0...v0.17.1

New Features

- Simulate data using `seismic +sim`:
- Reference sequences using `+sim ref`
- Secondary structures using `+sim fold`
- Parameters (mutation rates, end coordinate distributions, cluster proportions) using `+sim params`
- FASTQ files using `+sim fastq`
- All of the above (in that order) using `+sim total`
- Relate reports and datasets using `+sim relate`

Bug fixes

- Fixed a bug with the section name affecting ROC and rolling AUC-ROC graphs.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.16.5...v0.17.0

Bug fixes

- Prevent `seismic fold` from deleting the output file when `temp_dir` is the same as `out_dir`.
- In `seismic wf`, call the correct `RollingGiniRunner` class instead of its parent, `RollingStatRunner`.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.16.4...v0.16.5

New Features

- Graph rolling signal-to-noise ratios (i.e. AC versus GU) for DMS data with `seismic graph snrroll` (only relevant for `relate-per-pos.csv` tables).

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.16.3...v0.16.4

New Features

- Create rolling Gini coefficient graphs automatically via `seismic wf`.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.16.2...v0.16.3

New Features

- Graph the rolling Gini coefficient with `seismic graph giniroll`.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.16.1...v0.16.2