Seismic-rna

- Added Hatch targets to `pyproject.toml`
- Updated documentation

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.7.0...v0.7.1

- Output directories are now organized as `out/sample/step/ref` instead of `out/step/sample/ref`.
- Documentation has been partially updated.
- More unit tests have been added.
- A release schedule has been added.
- The --min-mapq option has been added.
- Log messages are color coded.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.6.2...v0.7.0

- Fixed bug with min_nmut_read not being accepted by `main.run()`

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.6.0...v0.6.2

- Graph Pearson or Spearman correlations between two samples in sliding windows.
- Fix bug involving missing arguments in `struct` module.

- Graph scatter plots and delta bar plots (i.e. the difference between two samples at each position) to visualize two mutational profiles over the same sequence.
- Plots comparing two samples, as well as comparing different sources of data (e.g. masked vs. clustered) within one sample, are supported.
- Plots involving two-sample comparisons are written to a sample directory named `{sample1}__and__{sample2}`.
- Both ratios and counts are supported.
- Stacked delta bar plots (breaking down differences between samples into each type of relation) are not supported.
- All graph types (except for stacked bar graphs) now support an option to normalize and winsorize ratiometric data (but not count-based data).
- This feature is especially useful for delta bar plots comparing two samples with different levels of DMS/SHAPE treatment.
- This feature works by specifying a quantile (`--quantile / -q`) in the range [0, 1] such that that quantile in the dataset is normalized to 1, all other data are scaled linearly, and any values greater than 1 (after scaling) are winsorized to 1.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.4.1...v0.5.0

- The column "Informed" has been added to table files explicitly.
- Primarily, this addition was the simplest way to resolve a bug wherein running `seismic graph seq -r n [TABLES ...]` would crash because the "Informed" column was not present in the table.
- Additionally, this step should reduce any misconceptions that the "Covered" column is used as the denominator for e.g. mutation ratios.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.4.0...v0.4.1