What's Changed

• Add option to cap concurrent partition count (#183)

• Use mauve format for partitioning mode and add VCF header for bcftools compatibility (#169 #177)
• Fix logged sequence lengths #173
• Use python3 in shebang line instead of python

Parsnp now outputs accurate CHROM and POS in the VCF output for multi-fasta references (they were previously being treated as a single concatenated sequence in terms of coordinates).

• Parsnp XMFA output now follows the Mauve format and has the appropriate header #FormatVersion Mauve so that HarvestTools parses it correctly. Fixes #169.
• Adds warning for multifasta reference VCF coordinates.

This release corrects the start location of reverse complement alignment records in the MAF output and also adds the ##maf version=1 program=parsnp header to the MAF output. The MAF output is now compliant with the UCSC format specification.

For more details, please see #167.

• The recombination filter has been fixed for partition workflows. Recombination filtering can now be enabled via --recomb-filter as well as the original -x, --xtrafast flags. Fixes #157.
• The --no-recruit has been fixed and replaced by --skip-ani-filter. Fixes #164.
• "Recruitment" in general has been renamed to "Filtering" to be consistent with other methods.
• Crashes gracefully when a partition's genomes are too divergent. Fixes #165.
• Inputs with duplicate filenames no longer allowed, i.e. /path1/genome.fna and /path2/genome.fna cannot both be provided. This is because the .xmfa and .maf output files use the file stem as the "sample" name. Fixes #166.

• Previously we were importing the extension module even if the user didn't need it. This required the pyspoa module and was causing issues. Now, users can run parsnp w/out pyspoa by using the --no-partition flag.
• Removes log redirects for harvest which cause crashes
• Uses regex strings for the parsers #153
• Adds back the gingr support for phipack results

• Parsnp now outputs a MAF file in addition to the typical XMFA file (can turn this off with (--no-maf).
• Parsnp now uses the partition mode by default when there are more than 100 input sequences.

• fasttree output is now moved to the correct spot for downstream processing (fixes #147)
• --min-ref-cov arg is now an inclusive lower bound instead of exclusive

• Replaces internal commands which were incompatible with MacOS.