Pypolca

* Adds `--careful` to log file to make it clear if it has been run

* Includes a number of changes by rrwick
* Fixes errors with counts in the report
* Fixes issue where pypolca would crash if there were spaces in the FASTA header
* Adds `--min_alt`, `--min_ratio` and `--careful` parameters
* Using --careful is recommended for low read depth (<25x coverage)

* Fixes bug in generating the report. If there were multiple alleles at a certain site (on a certain line in the vcf), this would crash pypolca. Exception handling has been added.
* Thanks oschwengers and npbhavya for detecting this

* Fixes bug where `pypolca` would warn it found 0 variants when in fact there were variants.
* Also would result in the polishing not working.
* Please upgrade if you have used v0.1.1!
* Importantly, this release adds benchmarking of `pypolca` v0.2.0 vs POLCA more thoroughly.

* Patch release to fix the release.yaml uploads to pypi.
* Also adds DOI with Zenodo

* Initial release


Usage: pypolca run [OPTIONS]

Python implementation of the POLCA polisher from MaSuRCA

Options:
-h, --help Show this message and exit.
-V, --version Show the version and exit.
-a, --assembly PATH Path to assembly contigs or scaffolds. [required]
-1, --reads1 PATH Path to polishing reads R1 FASTQ. Can be FASTQ or
FASTQ gzipped. Required. [required]
-2, --reads2 PATH Path to polishing reads R2 FASTQ. Can be FASTQ or
FASTQ gzipped. Optional. Only use -1 if you have
single end reads.
-t, --threads INTEGER Number of threads. [default: 1]
-o, --output PATH Output directory path [default: output_polca]
-f, --force Force overwrites the output directory
-n, --no_polish do not polish, just create vcf file, evaluate the
assembly and exit
-m, --memory_limit TEXT Memory per thread to use in samtools sort, set to
2G or more for large genomes [default: 2G]
-p, --prefix TEXT prefix for output files [default: polca]