Version 2.7.1

Bug fix writing Newick tree for Phandago when using Dendropy 4.2.0. Bug fixed, but now ariba requires dendropy >= 4.2.0 instead of previous 4.1.0.

Version 2.7.0

Added support for megares. https://megares.meglab.org/

Version 2.6.1

Bug fix reading some mlst files (should ignore more columns)

Version 2.6.0

• add support for MLST and getting schemes from pubmlst
• improve het snp calls by checking for strand bias

Version 2.5.1

Fix rare edge case where best assembly was not always being chosen, resulting in apparent truncated assemblies.

Version 2.5.0

Bug fixes:

• better choosing of closest reference sequnce
• minimap was not reporting hits for large clusters, so missing from final output
• some variants were being missed, and in the case of indels causing errors. Fixed by not using -C option of show-snps

Version 2.4.0

• improved how closest ref seq is chosen
• Mash no longer a dependency
• expose --threads option (but it is still experimental)
• "yes" and "yes_nonunique" now have same colour in phandango
• %identity column in report is now the % identity of the longest nucmer match between contig and reference (used to be mean% of all matches)

Version 2.3.0

• not backwards compatible. Files made by prepareref, and the report.tsv have changed.
• resfinder download using getref is fixed
• getref cleans up all temporary files (issue #135)
• getref has a new option --debug, which keeps all temporary files
• original sequence names are reported (issue #136)
• --force option added to the run task (issue #138)
• partial matches are reported by summary (issue #141)
• full codon change is reported in report.tsv (issue #142)
• uses $TMPDIR if it is set (issue #143)
• general improvements to reporting of samtools read depths and variant depths
• better filtering of read mapping before assembly
• extra checks to stop cases where extra copy of allele erroneously reported as partially present

Version 2.2.5

• improvements related to calling and reporting het variants
• remove dependency on samtools and bcftools
• remove unused code, was required before Mash was being used

Version 2.2.4

Bug fixes:

• reference sequences are renamed more aggressively, to stop third party tools dying
• various fixes involving reporting heterozygous snps