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Release 4.0.3 #154

Merged
merged 62 commits into from
Oct 29, 2024
Merged

Release 4.0.3 #154

merged 62 commits into from
Oct 29, 2024

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evolarjun
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This is an update for release 4.0.3 that includes StxTyper among other things.

Software and database format changes

  • See https://github.com/evolarjun/amr/wiki/New-in-AMRFinderPlus/ for more details.
  • StxTyper (https://github.com/ncbi/stxtyper) which accurately types full-length stx operons now included with AMRFinderPlus.
  • Database filename changes to standardize filenames and make writing scripts easier (See https://github.com/ncbi/amr/wiki/New-in-AMRFinderPlus for more information).
  • Column names in output have been changed to more closely other NCBI Pathogen Detection resources such as MicroBIGG-E.
  • Point mutations can now be reported with symbols different from the standard format.
  • The optional hierarchy_node field will now contain two node IDs for fusion proteins and stx operons separated by '::'.
  • The ability to have different curated blast cutoffs at multiple levels of the hierarchy with the same reference protein has been added.
  • The same protein can be used both as a reference gene to be reported and as the reference for point mutations.

Vyacheslav Brover and others added 30 commits February 12, 2024 15:48
Requires explicit rules for all object files, decided it isn't
worth fixing
…ove DOCUMENTATION and UPDATES sections to the end of the --help message
… for AMRProt was not found.'; PD-4926 StxTyper ver. 1.0.16; amr_report.cpp reports all stx genes
Update for Makefile changes from release version
evolarjun and others added 28 commits June 4, 2024 09:21
…ersion 1.0.21 is used; missing -db_gencode parameter is added to tblastn
Includes new tests for StxTyper and an addition to the usage message
to clarify that assembled nucleotide sequence is required. Hopefully
to reduce confusion as seen in Git issues 141 and 148.
…ver. 1.0.26; "::" is a fusion infix for hierarchy_node
Modified the subdirectory for StxTyper to stx and modified the
github_binary target to enable the installation of combined
AMRFinderPlus and StxTyper.
Re-enable downloading test data in `test_amrfinder.sh`
@evolarjun evolarjun merged commit e3007c0 into master Oct 29, 2024
0 of 4 checks passed
@evolarjun evolarjun deleted the stxtype branch October 30, 2024 16:04
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