Commits

History for

Commits on Jan 26, 2026

Version 4.2.7, fixes issue #180 PD-5549

authored

Commits on Sep 22, 2025

PD-5423 stop codon amino acid is changed: STOP -> Ter
Vyacheslav Brover
committed

Commits on Sep 12, 2025

PD-5427 [partial] fusion protein BLAST hit should be extended by >= 20 aa over a non-fusion protein hit to override it
Vyacheslav Brover
committed

Commits on Aug 19, 2025

JIRA PD-5426 bug in reporting strand by dna_mutation.cpp
Vyacheslav Brover
committed

Commits on Jul 22, 2025

PD-5394 only first gene disruption mutation is reported
Vyacheslav Brover
committed

Commits on Jul 16, 2025

PD-5393 subtype POINT should be preferred over POINT_DISRUPT; StxTyper ver. 1.0.45 of branch 'dev'
Vyacheslav Brover
committed

Commits on Jun 21, 2025

PD-5379 set subtype to POINT_DISRUPT for broken genes
Vyacheslav Brover
committed

Commits on May 19, 2025

PD-5329 Broken genes
Vyacheslav Brover
committed

Commits on Apr 14, 2025

PD-5299 --protein_output works with protein gzipped files
Vyacheslav Brover
committed

Commits on Feb 21, 2025

PD-5246 StxTyper ver. 1.0.42 of branch "dev"
Vyacheslav Brover
committed

Commits on Jan 10, 2025

PD-5215 StxTyper ver. 1.0.29 of branch "gpipe_compat"
Vyacheslav Brover
committed

Commits on Dec 15, 2024

PD-5191 StxTyper ver. 1.0.30, stxtyper --threads
Vyacheslav Brover
committed

Commits on Dec 9, 2024

PD-5181: StxTyper ver. 1.0.28
Vyacheslav Brover
committed

Commits on Nov 13, 2024

colorizeDir(); prohibit --database_version and -p or -n; GCC 13.2.0
Vyacheslav Brover
committed

Commits on Oct 22, 2024

PD-5156 version 4.0.0
Vyacheslav Brover
committed

Commits on Aug 5, 2024

PD-5076 StxTyper version 1.0.24
Vyacheslav Brover
committed

Commits on Jul 25, 2024

PD-5054 Check that the file AMR_DNA-<organism>.ndb exists; StxTyper version 1.0.21 is used; missing -db_gencode parameter is added to tblastn
Vyacheslav Brover
committed

Commits on May 21, 2024

PD-5002 StxTyper ver. 1.0.20
Vyacheslav Brover
committed

Commits on May 6, 2024

PD-4981 susceptible/point mutation collision
Vyacheslav Brover
committed

Commits on Mar 5, 2024

PD-4910 integrate StxTyper
Vyacheslav Brover
committed

Commits on Feb 27, 2024

PD-4888 mutate.cpp is added
Vyacheslav Brover
committed

Commits on Feb 21, 2024

PD-4906 --print_node for fusion proteins
Vyacheslav Brover
committed

Commits on Feb 13, 2024

PD-4893 move DOCUMENTATION section to the end of the usage message; move DOCUMENTATION and UPDATES sections to the end of the --help message
Vyacheslav Brover
committed

Commits on Feb 12, 2024

PD-PD-4874 -v == --version
Vyacheslav Brover
committed

Commits on Jan 19, 2024

PD-4856 Allow multiple Blast Rules for the same protein
Vyacheslav Brover
committed

Commits on Dec 18, 2023

PD-4838 adding '*' to the ends of reference proteins
Vyacheslav Brover
committed

Commits on Oct 6, 2023

PD-4764 Remove '*' from Prodigal output to ensure ALLELEP and EXCATP matches
Vyacheslav Brover
committed

Commits on Oct 5, 2023

PD-4754 prodigal; PD-4761 proteins with >= 20 Xs from the input protein FASTA file are removed
Vyacheslav Brover
committed

Commits on Oct 2, 2023

PD-4755 calling fusion2geneSymbols() for a mutation protein
Vyacheslav Brover
committed

Commits on Sep 6, 2023

PD-4722 bug: calling fusion2geneSymbols() for a mutation protein; color codes are printed only when output is to screen
Vyacheslav Brover
committed

Commits on Aug 9, 2023

PD-4698 if a pseudogene is overlapped by a different gene on the length >= 20 aa then the pseudogene is not reported
Vyacheslav Brover
committed

Commits on Aug 4, 2023

PD-4706 protein match overrides a nucleotide match for point mutations
Vyacheslav Brover
committed

Commits on Jul 19, 2023

PD-4687 distinct overlapping hits are not reported separately for protein targets for the same alleles or gene symbols
Vyacheslav Brover
committed

Commits on Jul 18, 2023

get_threads_max_max() for __APPLE__
Vyacheslav Brover
committed
PD-4687 distinct overlapping hits are not reported separately for protein targets
Vyacheslav Brover
committed