Seismic-rna

Bug Fixes

- Simulated relate batches (`seismic +sim relate`) now drop reads with zero coverage, preventing an error during the `table` step.
- Coverage calculation can now handle cases where the mask is `False` rather than an array.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.17.3...v0.17.4

New Features

- `seismic wf` now has options `--graph-xyz` / `--no-graph-xyz` to control whether each type of graph xyz is generated. By default, mutational profiles, typed mutational profiles, coverage profiles, and histograms of mutations per read are graphed, as are ROC curves and rolling AUC-ROC if `--fold` is also used. Rolling Gini is no longer graphed by default but can be enabled with `--graph-giniroll`.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.17.2...v0.17.3

New Features

- Clip bases from the 5' and 3' ends of reads (`--clip-end5` and `--clip-end3`) to fix bias caused by alignment. Substitutions within several bases of the end of a read will be soft-clipped in local mode (`--bt2-local`), and indels are will be forbidden entirely (depending on `--bt2-gbar`). Consequently, such mutations will be dropped during alignment, and bases close to the ends of a read will only be matches, overall deflating the mutation rates (especially at the 5'/3' ends ends of reference sequences). To correct this bias, several bases can be clipped from the 5' and 3' ends of each read. By default, 4 bases are clipped from the 5' ends because that is the default of `--bt2-gbar`; and 6 bases are clipped from the 3' ends because random primers are typically hexamers (6 bases).
- Demultiplexed FASTQ files can now also be given as files, not just as directories.
- Paired-end FASTQ files can now also have labels `_1` and `_2`.

Interface Changes

- Rename the temporary from `temp` to `tmp` and rename all pertinent options (e.g. `--keep-temp` to `--keep-tmp`) to make it the same length as `out` and to avoid confusion with "temperature" (e.g. in `--fold-temp`).

Bug Fixes

- Fix bug causing datasets with zero reads and/or positions to crash during `cluster` and `table`.
- Fix bug with attributes during tabulation of joined clusters.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.17.1...v0.17.2

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