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Commits on Sep 4, 2024

• replace with modular codebase

  Marysteph

  authored
  ab9c7ad

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Commits on Sep 3, 2024

• replace with modular codebase

  katholt

  committed
  11a8785

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Commits on Jan 2, 2024

• fixing shv tests

  

  Kara Tsang

  committed
  6eb0fc9

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Commits on Jan 23, 2023

• Rename CARD name in tests

  rrwick

  committed
  31cf53b

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Commits on Nov 15, 2021

• Get K and O types from Kaptive

  rrwick

  committed
  a3dd7e7

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Commits on May 20, 2021

• Label virulence loci with truncated genes

  rrwick

  committed
  809bcf3

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Commits on May 12, 2021

• Update species identification database

  rrwick

  committed
  7da21f7

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Commits on Mar 10, 2021

• Report Kaptive loci below a minimum confidence threshold as unknown

  rrwick

  committed
  93a303c

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Commits on Feb 9, 2021

• New tests for alternate stop codon exact amino acid match

  rrwick

  committed
  63c23e7

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• New tests for alternate stop codon exact amino acid match

  rrwick

  committed
  4b9c5a6

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Commits on Feb 2, 2021

• Allow for contained matches in exact amino acid check

  rrwick

  committed
  7fda06e

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Commits on Feb 1, 2021

• Adjust exact amino acid match logic

  rrwick

  committed
  6d79d73

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Commits on Jan 28, 2021

• Add new tests for BLAST-related bug

  rrwick

  committed
  1515505

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Commits on Oct 22, 2020

• Add O_type column

  rrwick

  committed
  2f85330

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Commits on Sep 10, 2020

• 1LV still allows for ozaenae/rhinoscleromatis call

  rrwick

  committed
  ac26f8d

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• Add other STs to ozaenae/rhinoscleromatis

  rrwick

  committed
  1a73c51

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Commits on Sep 9, 2020

• Fix typo: ozanae -> ozaenae

  rrwick

  committed
  9cc1746

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Commits on Aug 17, 2020

• Change mutation notation

  rrwick

  committed
  adf8939

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Commits on Aug 11, 2020

• Include the Col_mutations column when calculating resistance score

  rrwick

  committed
  a58079b

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Commits on Aug 7, 2020

• SHV mutations can downgrade Bla class

  rrwick

  committed
  eff403b

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• New column for truncated resistance genes

  rrwick

  committed
  eb6f80f

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Commits on Jul 31, 2020

• Change Bla_broad alleles to Bla

  rrwick

  committed
  6104011

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Commits on Jul 30, 2020

• Put a dash for all empty SHV mutations

  rrwick

  committed
  ab4524f

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• Fix class count test

  rrwick

  committed
  7c69091

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• Change QRDR_mutations to Flq_mutations

  rrwick

  committed
  df505e1

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• Check for SHV mutations

  rrwick

  committed
  2d0fa00

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Commits on Jul 28, 2020

• Add acquired to column names

  rrwick

  committed
  c6f2985

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Commits on Jul 21, 2020

• Move colistin-causing truncations to Col_mutations column

  rrwick

  committed
  2f160b6

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• Move QRDR mutations into their own column

  rrwick

  committed
  bb744d7

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Commits on Jul 17, 2020

• Change test name

  rrwick

  committed
  0242592

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Commits on Jul 9, 2020

• Truncated resistance genes go to the spurious hits column

  rrwick

  committed
  080dfd4

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Commits on Jul 3, 2020

• Change Omp column to Omp_truncations

  rrwick

  committed
  918aa1a

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Commits on Jun 11, 2020

• Fix up unit tests for recent changes

  rrwick

  committed
  196cbaa

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Commits on Mar 23, 2020

• Don't include spurious hits in gene/class counts

  rrwick

  committed
  8c510af

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• Add MGE to RmpADC lineages

  rrwick

  committed
  b9d0af4

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