6.0.8

Updated diamond and used fixmate for bwt

6.0.7

• Fixed Invalid BAM file error when running rgi kmer_query
• Added support for newer versions of diamond
• Updated docs and threads args to be consistent

6.0.6

• deprecate split_prodigal_jobs command
• modify clean to support Python versions < 3.11
• patch for longer ORF predicted by Prodigal
• Added an option to load CARD canonical only when using rgi auto_load command
• Reset SNPList when generating CARD databases
• Update documentation

6.0.5

• Updated to write .ncbirc config once
• Added AST_Source column for mutations
• Fixed contig column and regex typo
• Switched to handling nucleotides snps in lowercase

6.0.4

• Updated versions used for BLAST, Pyrodigal, KMA, samtools, and libs
• Support for Var and Ter mutations
• Fixed Runtime Error
• Added more tests

6.0.3

• adds hit coordinates to the start and end of gene coordinates
• adds antibiotics to the tab-separated output file
• switch to using GitHub actions for testing
• adds BLAST config file

6.0.2

• Adds support for Pyrodigal
• Adds new CARD 2023 citation

6.0.1

• Fixed kmer query failed to parse BAM file issue
• Fixed infinite loop if the FASTA file is empty
• Updated cleaned files and auto load print statements

6.0.0

• Added an option (--keep) to keep Prodigal CDS when used with --clean
• Removed option --exclude_nudge and replaced with --include_nudge
• Added options to use all CARD models with rgi bwt, by default rgi bwt use homolog models only
• Added dask and replace some os.system calls to improve performance
• Consensus sequences are reported at depth of at least 5 when using rgi bwt with KMA
• Updated rgi load and rgi auto_load commands

5.2.1

• Updated biopython to 1.78 and lxml to 4.6.5
• Updated READMEs and CITATIONS
• Updated hardcoded paths to be configurable
• Fixed channel order