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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

Commits on Feb 12, 2024

  1. PD-PD-4874 -v == --version

    Vyacheslav Brover committed Feb 12, 2024
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Commits on Feb 13, 2024

  1. Make COMPILE.cpp explicit 

    #130
    @evolarjun
    evolarjun committed Feb 13, 2024
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  2. Reverting Makefile fix 

    Requires explicit rules for all object files, decided it isn't
worth fixing
    @evolarjun
    evolarjun committed Feb 13, 2024
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  3. PD-4893 move DOCUMENTATION section to the end of the usage message; m… 

    …ove DOCUMENTATION and UPDATES sections to the end of the --help message
    Vyacheslav Brover committed Feb 13, 2024
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Commits on Feb 21, 2024

  1. PD-4906 --print_node for fusion proteins

    Vyacheslav Brover committed Feb 21, 2024
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Commits on Feb 27, 2024

  1. PD-4888 mutate.cpp is added

    Vyacheslav Brover committed Feb 27, 2024
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  2. PD-4888 mutate.cpp is added

    Vyacheslav Brover committed Feb 27, 2024
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Commits on Mar 4, 2024

  1. Added stxtyper as a submodule

    @evolarjun
    evolarjun committed Mar 4, 2024
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  2. Updated Makefile to also make StxTyper

    @evolarjun
    evolarjun committed Mar 4, 2024
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  3. Test to see if I can get svn checkout correct

    @evolarjun
    evolarjun committed Mar 4, 2024
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  4. Fix GitHub actions for submodule stxtyper

    @evolarjun
    evolarjun committed Mar 4, 2024
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Commits on Mar 5, 2024

  1. PD-4910 integrate StxTyper

    Vyacheslav Brover committed Mar 5, 2024
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  2. StxTyper 1.0.13

    Vyacheslav Brover committed Mar 5, 2024
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  3. PD-4910 stxtyper ver. 1.0.14: --print_node; stxtyper -q

    Vyacheslav Brover committed Mar 5, 2024
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Commits on Mar 8, 2024

  1. PD-4923 Verify the version of StxTyper when AMRFinderPlus is run

    Vyacheslav Brover committed Mar 8, 2024
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Commits on Mar 13, 2024

  1. PD-4925 more detailed explanation for the message 'The BLAST database… 

    … for AMRProt was not found.'; PD-4926 StxTyper ver. 1.0.16; amr_report.cpp reports all stx genes
    Vyacheslav Brover committed Mar 13, 2024
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Commits on Apr 5, 2024

  1. Update version of stxtyper

    @evolarjun
    evolarjun committed Apr 5, 2024
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  2. Update action to handle change in output

    @evolarjun
    evolarjun committed Apr 5, 2024
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Commits on Apr 9, 2024

  1. stxtyper 1.0.19

    Vyacheslav Brover committed Apr 9, 2024
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  2. Merge branch 'stxtype' of https://github.com/ncbi/amr into stxtype

    Vyacheslav Brover committed Apr 9, 2024
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Commits on May 6, 2024

  1. PD-4981 susceptible/point mutation collision

    Vyacheslav Brover committed May 6, 2024
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Commits on May 8, 2024

  1. Update hash for stxtyper

    @evolarjun
    evolarjun committed May 8, 2024
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  2. Updated README.md with compilation instructions

    @evolarjun
    evolarjun committed May 8, 2024
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  3. Debugging commands for GitHub action

    @evolarjun
    evolarjun committed May 8, 2024
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  4. Attempted workflow test fix

    @evolarjun
    evolarjun committed May 8, 2024
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  5. Fix and clean up actions

    @evolarjun
    evolarjun committed May 8, 2024
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  6. Updated install instructions in README

    @evolarjun
    evolarjun committed May 8, 2024
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Commits on May 20, 2024

  1. Merge pull request #143 from ncbi/master 

    Update for Makefile changes from release version
    @evolarjun
    evolarjun authored May 20, 2024
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Commits on May 21, 2024

  1. PD-5002 StxTyper ver. 1.0.20

    Vyacheslav Brover committed May 21, 2024
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Commits on May 22, 2024

  1. Updates for version 1.0.20 of stxtyper

    @evolarjun
    evolarjun committed May 22, 2024
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  2. PD-5004 a regular reference protein can have point mutations

    Vyacheslav Brover committed May 22, 2024
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Commits on Jun 3, 2024

  1. PD-5014 duplicate susceptible proteins are not reported

    Vyacheslav Brover committed Jun 3, 2024
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  2. Update stxtyper

    @evolarjun
    evolarjun committed Jun 3, 2024
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  3. PD-5015 HMMs are not applied to mutation proteins; -db_gencode parame… 

    …ter is added to tblastn; PD-4969 redundant QC check is removed
    Vyacheslav Brover committed Jun 3, 2024
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Commits on Jun 4, 2024

  1. Minor Makefile updates

    @evolarjun
    evolarjun committed Jun 4, 2024
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  2. Unknown stxtyper hash update

    @evolarjun
    evolarjun committed Jun 4, 2024
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  3. Change build for github_binaries to /usr/bin/g++ 

    PD-4946
    @evolarjun
    evolarjun committed Jun 4, 2024
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Commits on Jun 5, 2024

  1. Updated github_binaries target to include stxtyper

    @evolarjun
    evolarjun committed Jun 5, 2024
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Commits on Jun 6, 2024

  1. Restoring make clean to github_binaries target

    @evolarjun
    evolarjun committed Jun 6, 2024
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Commits on Jul 25, 2024

  1. PD-5054 Check that the file AMR_DNA-<organism>.ndb exists; StxTyper v… 

    …ersion 1.0.21 is used; missing -db_gencode parameter is added to tblastn
    Vyacheslav Brover committed Jul 25, 2024
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Commits on Jul 29, 2024

  1. PD-5064 StxTyper version 1.0.23; URLs in messages are in blue color

    Vyacheslav Brover committed Jul 29, 2024
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Commits on Aug 2, 2024

  1. Link stxtyper to latest dev version

    @evolarjun
    evolarjun committed Aug 2, 2024
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Commits on Aug 5, 2024

  1. PD-5076 StxTyper version 1.0.24

    Vyacheslav Brover committed Aug 5, 2024
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Commits on Aug 6, 2024

  1. Updates to stxtyper

    @evolarjun
    evolarjun committed Aug 6, 2024
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  2. new stxtyper

    Vyacheslav Brover committed Aug 6, 2024
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  3. Pin to latest stxtyper commit

    @evolarjun
    evolarjun committed Aug 6, 2024
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Commits on Aug 15, 2024

  1. PD-5084 mutation_std, mutation_reported; PD-5091 .fa, .tsv

    Vyacheslav Brover committed Aug 15, 2024
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  2. Pin to latest changes for StxTyper

    @evolarjun
    evolarjun committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. PD-5085 new AMRFinderPlus column names

    Vyacheslav Brover committed Aug 16, 2024
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Commits on Aug 17, 2024

  1. PD-5085 columns.hpp

    Vyacheslav Brover committed Aug 17, 2024
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Commits on Sep 11, 2024

  1. Minor updates to StxTyper and usage message 

    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.
    @evolarjun
    evolarjun committed Sep 11, 2024
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Commits on Oct 18, 2024

  1. Pin to StxTyper v1.0.25

    @evolarjun
    evolarjun committed Oct 18, 2024
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  2. Update test data for new version

    @evolarjun
    evolarjun committed Oct 18, 2024
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Commits on Oct 22, 2024

  1. PD-5156 version 4.0.0

    Vyacheslav Brover committed Oct 22, 2024
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  2. PD-5085: Change column "Element length" to "Target length"; StxTyper … 

    …ver. 1.0.26; "::" is a fusion infix for hierarchy_node
    Vyacheslav Brover committed Oct 22, 2024
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Commits on Oct 23, 2024

  1. PD-5155 StxTyper version 1.0.27

    Vyacheslav Brover committed Oct 23, 2024
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Commits on Oct 26, 2024

  1. Update test data for version 4.0.2

    @evolarjun
    evolarjun committed Oct 26, 2024
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Commits on Oct 27, 2024

  1. Modifications to facilitate installation 

    Modified the subdirectory for StxTyper to stx and modified the
github_binary target to enable the installation of combined
AMRFinderPlus and StxTyper.
    @evolarjun
    evolarjun committed Oct 27, 2024
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Commits on Oct 28, 2024

  1. Added an stx operon to the test suite

    @evolarjun
    evolarjun committed Oct 28, 2024
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Commits on Oct 29, 2024

  1. PD-5167 Don't error out when using older blast+

    @evolarjun
    evolarjun committed Oct 29, 2024
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  2. Forgot to update the version number to 4.0.3

    @evolarjun
    evolarjun committed Oct 29, 2024
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  3. Update test_amrfinder.sh 

    Re-enable downloading test data in `test_amrfinder.sh`
    @evolarjun
    evolarjun authored Oct 29, 2024
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