Seismic-rna

- 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

- In the steps that use a FASTA file of reference sequences, the file is now a required positional argument.
- In the `align` step, `-x` now means paired-end and `-z` now means single-end (and likewise for `-X` and `-Z`).
- A rudimentary user manual has been added.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.3.0...v0.4.0

- Files of input data (alignment maps, reports, tables, etc.) are now positional arguments instead of options. Thus, they can be given a) without a flag and b) using shell wildcard completion. The latter feature is more important, as it allows one to give arbitrary files that match a shell wildcard rather than specifying each file individually. For example, `table out/report/sample3*` instead of the much more verbose `table -i out/report/sample31 -i out/report/sample32 -i out/report/sample33 -i out/report/sample34 -i out/report/sample35`.
- The __version__ attribute now exists, though a bug still causes its value to default to `"unknown"`. Likewise, `srna --version` now produces output without crashing.

Why this is a minor release (v0.3.0) instead of a patch (v0.2.1)

The change in specifying input files on the command line interface causes a significant change in the command line interface for all steps except `align`. Since I increment patch numbers for smaller changes (e.g. minor bug fixes, internal optimizations) and minor version numbers for medium changes (e.g. affecting the user interface), this release fit better as a new minor version.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.2.0...v0.3.0

- Generate graphs from cluster tables using `graph seq`, in the same manner as for tables from the relate and mask steps. Multiple types of relationships can likewise be stacked with the `--stack` option, and the y-axis can be toggled between ratios and counts. The `--arrange` option controls whether one cluster is graphed per file, all clusters from one order are graphed per file, or all clusters from all orders are graphed in one file.
- In graphing, rename "fraction" to "ratio" (which is shorter, and the same length as "count") and rename the option from `--yfrac` to `--y-count`.
- Update the color palettes for graphs to be more aesthetically pleasing and more accessible for people with impaired color vision.
- Introduce the command line option `--input-file` (`-i`) to unify the separate command line options for alignment map (BAM) files (previously `-b`), report files (previously `-r`), and table files (previously `-t`). The aim is to eliminate confusion among these options and free up the `-r` and `-t` short options.
- Change the short versions of command line options, including sequence read (FASTQ) files (`-s` -> `-x`, `-i` -> `-y`, and `-m` -> `-z`, as well as the uppercase versions), the temporary directory (newly `-t`), and table/graph relationships (`-c` -> `-r`).
- Introduce a new logo for SEISMIC-RNA, as well as the source code that generates it (`seismicrna/logo/logo.py`).

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.1.3...v0.2.0