Releases: marbl/parsnp
Releases · marbl/parsnp
Release v2.0.5
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.
Release v1.7.4
- abpoa and muscle have been replaced by
mafft
for inter-LCB alignment.
Release v1.7.3
The --extend-lcbs
parameter now performs a gapped alignment using either muscle (>50nt) or abpoa (<=50nt) on inter-LCB regions. Alignments are trimmed back based on an ANI parameter that can also be provided by the user (i.e., cuts alignment off when it falls below 95% ANI). This parameter still only works w/ single contig genomes.
Also added better SeqIO
validation. Throws out any genomes that can't be parsed.
Release v1.7.2
- Fix bug where Harvesttools is provided both a gbk and fasta reference.
v1.7.1
- Mismatch=-4 and gap=-2 for extending LCBs
- Fixed bug that created extra gaps in LCB extension
- Fixed bug that resulted in FastTree being used in cases when it wasn't requested
- Fixed bug that duplicated reference in alignment output
- Reference sequence is now first in extended xmfa output