v2.1.2

• 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.

v2.1.1

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.

v2.1.0

• 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.

Parsnp v2.0.6

• 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

Release v2.0.5

• 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.

Release v2.0.4

• 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

Release v2.0.3

• Replaces internal commands which were incompatible with MacOS.

Release v2.0.2

• The interval for each xmfa record is now inclusive, following the xmfa format. This only effects the internal coordinate representation, used by gingr. The s[seq_idx]:p[position] coordinates remain unchanged.
• tqdm logging has been redirected to the Parsnp logger
• The extension module now also uses SPOA. However, it is still experimental.
• Extension is much more conservative than before, but still can produce less conserved alignments

Release v2.0.1

• Output is now deterministic, even in partition mode
• time is now only prepended to commands if it exists on the system

Parsnp v2.0.0

What's Changed

• You can now pass a newline-separated file of paths to query sequences to -d in addition to directories and command-line lists.
• Adds --partition flag, which splits recruited genomes into partitions of size --partition-size (default 50).
• Adds --no-recruit option which skips the recruitment step, but still drops genomes if their size differs substantially from the reference.
• Fixes multiple bugs in the output:
  • Output can now be parsed by BioPython's AlignIO module with the "mauve" format
  • LCBs no longer overlap
  • Ambiguous base pairs and small contigs no longer lead to incorrect coordinates
  • VCF now contains the correct reference allele.
• FastANI now guarantees at least 100 segments (unless it requires a fragment length < 500)
• Adds --min-ref-cov option (default 90), which when used with --use-ani, removes query genomes that do not cover at least 90% of the reference.
• Output folder has been reorganized to separate logs and config files from the main output.