0.3.1

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

v0.3.0

• 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)

v0.2.1

• 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

v0.2.0

• 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.

v0.1.1

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

v0.1.0 9 October 2023

• 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]