Plassembler

------------------

* Adds `--no_chromosome` option to `plassembler long` and `plassembler run` after a request to allow for the assembly of read sets that have only plasmids.
* Using this will skip Flye and create a dummy 3MB chromosome full of A's.
* Fixes another bug here [issue](https://github.com/gbouras13/plassembler/issues/37).

------------------

* `plassembler long` should yield improved results. It achieves this by treating long reads as both short reads (in the sense of creating a de Brujin graph based assembly) and long reads (for scaffolding) in Unicycler.
* While I'd still recommend short reads if you can get them, I am now confident that if your isolate has small plasmids in the long read set, `plassembler long` should find them.
* For more information, see the [documentation](https://plassembler.readthedocs.io/en/latest/long/).
* The ability to specify a `--flye_assembly` and `--flye_info` if you already have a Flye assembly for your long reads instead of `--flye_directory` has been added. Thanks to [incoherentian](https://github.com/incoherentian)'s [issue](https://github.com/gbouras13/plassembler/issues/37)
* The ability to specify a `--no_copy_numbers` with `plassembler assembled` if you just want to run some plasmids against the PLSDB has been added. Thanks to [gaworj](https://github.com/gaworj)'s [issue](https://github.com/gbouras13/plassembler/issues/36).

* `plassembler long` officially released and implemented using [Canu](https://github.com/marbl/canu) and [dnaapler](https://github.com/gbouras13/dnaapler) to reassemble unmapped reads in place of Unicycler for `plassembler run`. While we'd still recommend getting short reads if you really want to recover plasmids, as long as your long reads are short enough (i.e. not size selected), `plassembler long` should hopefully recover most small plasmids.
* For more information, see the [documentation](https://plassembler.readthedocs.io/en/latest/long/).
* Faster mapping thanks to [fanvanf](https://github.com/fanvanf)'s [issue](https://github.com/gbouras13/plassembler/issues/29).
* The ability to specify a `--flye_directory` if you already have a Flye assembly for your long reads, which will tell `plassembler` to skip the long read assembly step.

------------------

* Refactored codebase and release on pypi
* Adds unit tests and CI
* Replace `argparse` with `click`
* Adds option to skip chopper and fastq to `plassembler run` using `--skip_qc`
* Breaking CLI changes to be compatible with click
* `plassembler.py` changed to `plassembler run`
* Adds Raven long read assembly option to `plassembler run` using `--use_raven`
* `install_database.py` changed to `plassembler download`
* Assembled mode now `plassembler assembled`
* Untested/experimental long read only mode using `plassembler long`
* Removes rasusa, `-s` and `--no_subsample`. If users want faster runtimes, we recommend `--use_raven` or conduct subsampling prior.

------------------

* Large overhaul.
* Adds `--pacbio_model` for pacbio data
* Replaces nanofilt with chopper
* Adds `-a` for assembled mode
* Adds subsampling with rasusa, and `-s` to change subsampling depth, and `--no_subsample` to turn off subsampling
* Adds `--keep_fastqs`
* Adds `--keep_chromosome`
* Refactors mapping code
* Adds custom function to identify multimapped reads
* Changes output formats - consolidates all output into `summary.tsv`.

------------------

* Adds checks for dependencies.
* Adds samtools to bioconda recipe (thanks Jan/gaworj).
* Adds long-only kmer_mode for very high quality Nanopore reads (R10.4 and above) - experimental until I get more data especially with small plasmids. Does exactly the same (Flye -> Unicycler). Seems to work pretty well.