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0.2.0
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@apetkau apetkau released this 05 Jun 19:03
· 629 commits to development since this release
0.2.0
6f42299
  • Major
    • Inclusion of predicted resistances to antimicrobial drugs thanks to gene/drug mappings from the NARMS/CIPARS Molecular Working Group. Resistance predictions are microbiological resistances and not clinical resistances (issue #4, #6).
    • Adding a staramr db restore-default command to restore the default staramr database (issue #3).
    • Switched to using BLAST Tabular data + pandas to read BLAST results (issue #10).
    • Inverted direction of BLAST (we now BLAST the AMR gene files against the input genomes).
  • Minor
    • Less verbose messages when encountering errors parsing the command-line options.
    • Able to support adding options after a list of files (e.g., staramr search *.fasta -h will print help docs).
    • Switched to including negative AMR results (samples with no AMR genes) by default. Must now use parameter --exclude-negatives to exclude them (issue #2).
    • Only print 2 decimals in Excel output (issue #5).
    • Automatically adjust Excel cells to better fit text (issue #7).
    • Many other coding improvements (issue #11, #13 and others).
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