Pyroe

Add aliases for `make-splici` and `make-splcieu`:

* `make-spliced+intronic` can be used as an alias for `make-splici`
* `make-spliced+unspliced` can be used as an alias for `make-spliceu`

Added `make-spliceu` command.

Rename `gene_name_to_id.tsv` output of `make-splici` to `gene_id_to_name.tsv` to match the actual order of the columns in the file.

This release improves the robustness of GTF parsing, adds the `--write-clean-gtf` flag to the `make-splici` command, and adds an extra output (a gene-id to gene-name mapping) as the result of the `make-splici` command.

**Full Changelog**: https://github.com/COMBINE-lab/pyroe/compare/v0.6.0...v0.6.3

This release adds a `-v` and `--version` flag to `pyroe`.

**Full Changelog**: https://github.com/COMBINE-lab/pyroe/compare/v0.6.0...v0.6.2

This release fixes a bug in the reading a temporary fast file in the calling of `bedtools`, it adds no new functionality.

**Full Changelog**: https://github.com/COMBINE-lab/pyroe/compare/v0.6.0...v0.6.1