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florianzwagemaker wants to merge 36 commits intodevRIVM-bioinformatics/AmpliGone:devfrom 2.0.0RIVM-bioinformatics/AmpliGone:2.0.0Copy head branch name to clipboard

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Commits on Apr 2, 2024

• refactor: change the entrypoint file from AmpliGone.py to __main__.py

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Commits on May 25, 2024

• ci: update publish and release workflows

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• deps: update dependencies in setup.py and env.yml

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• deps: update minimum required python version in setup.py

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• refactor: move program name and version to __init__.py

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• refactor: move logger function to its own file (log.py)

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• refactor: move argument parser to its own file including helpdoc formatter (args.py)

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• refactor: remove func.py

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• refactor: take the application name from the __prog__ variable in setup.py

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• refactor: move the functionality of alignment preset from mappreset.py to alignmentpreset.py for clearer filenaming

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• refactor: change the imports in fasta2bed to not be relative imports but static imports to improve stability

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• fix: change the table of IUPAC data to actually reference the IUPACData table in fasta2bed

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• refactor: change name of MakeCoordinateLists method to find_or_read_primers

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• feat: add the --verbose flag and debugging log messages

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• style: formatting with isort & black

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• deps: add pgzip to the dependency list

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• feat: add the 'virtual primer support' to link closely positioned primers to each other in the index for accurate removal

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Commits on Jul 11, 2024

• feat: add quiet mode, only prints WARNING and ERROR log messages

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• refactor: add verbose mode (debugging) to standalone args of fasta2bed module

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• feat!: change fasta2bed method from fuzzyregex to semi-global alignment based search with parasail

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• refactor: remove the extended regex library from AmpliGone.args and use the normal included re library

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• deps: update dependencies in env.yml

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• fix: proper grouping of the regex to clean cigar strings

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Commits on Jul 22, 2024

• fix: do not update per-thread progression when processing very low read counts (will throw zerodivisionerror)

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Commits on Aug 15, 2024

• fix: improve error message when too little threads are given

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• docs: expand function docstring to better explain the edge cases

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Commits on Oct 23, 2024

• test: started testing

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Commits on Oct 28, 2024

• test: tests/e2e/ - added simple end-to-end test for AmpliGone

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Commits on Oct 29, 2024

• refactor: represent the primer-alignment in a percentage of matches or as alignment-score in bedfile

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Commits on Nov 12, 2024

• Merge branch '2.0.0' into sonarcloud-branch-analysis

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• Merge branch 'static-analysis' into sonarcloud-branch-analysis

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• feat: sonar-project.properties - added branch analysis config

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Commits on Dec 31, 2024

• test: finished unit tests for arg_parse, cut_reads, cutlery, and fasta2bed.

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• Merge branch 'pipeline-test-suite' into test-suite

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• fix: fixed a typo in fasta2bed

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Commits on Feb 14, 2025

• Merge pull request #85 from RIVM-bioinformatics/test-suite

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