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ieeta-pt / VCFX Public

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Dev#3

Closed

jorgeMFS wants to merge 108 commits into

ieeta-pt:mainieeta-pt/VCFX:mainfrom

jorgeMFS:devjorgeMFS/VCFX:devCopy head branch name to clipboard

Conversation Commits108 (108)Checks Files changed

Closed

Dev#3
jorgeMFS wants to merge 108 commits into
ieeta-pt:mainfrom
jorgeMFS:dev

Commits

Commits on May 21, 2025

Fix NaN output in quality adjuster
jorgeMFS
committed
Merge pull request #1 from jorgeMFS/codex/find-and-fix-bug
jorgeMFS
authored
Fix Emscripten build detection
jorgeMFS
committed
Merge pull request #2 from jorgeMFS/codex/fix-broken-webassembly-build-configuration
jorgeMFS
authored
fix: support modern find in path script
jorgeMFS
committed
Merge pull request #3 from jorgeMFS/codex/fix-invalid-mode-in-add_vcfx_tools_to_path.sh
jorgeMFS
authored
fix: ensure newline at EOF for .dockerignore
jorgeMFS
committed
Merge pull request #4 from jorgeMFS/codex/fix-.gitignore-missing-newline
jorgeMFS
authored
Optimize alignment checker memory usage
jorgeMFS
committed
Merge pull request #5 from jorgeMFS/codex/verify-reference-genome-naming-logic
jorgeMFS
authored
Make haplotype extractor debug output optional
jorgeMFS
committed
Merge pull request #6 from jorgeMFS/codex/remove-unconditional-stderr-output
jorgeMFS
authored
Add trailing newline to Dockerfile and CMakeLists
jorgeMFS
committed
Merge pull request #7 from jorgeMFS/codex/append-newline-to-cmakelists.txt-and-dockerfile
jorgeMFS
authored
Add basic utilities to vcfx_core
jorgeMFS
committed
refactor merger to stream
jorgeMFS
committed
Merge pull request #8 from jorgeMFS/codex/provide-reusable-utilities-or-drop-library
jorgeMFS
authored
Merge pull request #9 from jorgeMFS/codex/refactor-mergevcf-to-process-files-line-by-line
jorgeMFS
authored
Fix merger sort for unsorted inputs
jorgeMFS
committed
Merge pull request #10 from jorgeMFS/codex/fix-stray-prompts-and-validate-yaml-in-workflows
jorgeMFS
authored
Add CI workflow to build and test
jorgeMFS
committed
Merge pull request #11 from jorgeMFS/codex/add-ci-workflow-for-cmake-project
jorgeMFS
authored

Commits on May 22, 2025

docs: reference public container
jorgeMFS
committed
Add gzip support and tests
jorgeMFS
committed
Merge pull request #13 from jorgeMFS/codex/add-helper-functions-for-compressed-streams
jorgeMFS
authored
Merge pull request #12 from jorgeMFS/codex/fix-vcfx-docker-pull-issue
jorgeMFS
authored
test: skip Docker tests if Docker missing
jorgeMFS
committed
Update test_docker.sh
jorgeMFS
authored
Update test_docker.sh
jorgeMFS
authored
Merge pull request #14 from jorgeMFS/codex/introduce-vcfx_image-variable-in-test_docker.sh
jorgeMFS
authored
Add strict mode validation for VCFX_validator
jorgeMFS
committed
Merge pull request #15 from update-vcfx_validator-for-strictmode
jorgeMFS
authored
Integrate shell scripts with CTest
jorgeMFS
committed
Merge pull request #16 from update-cmakelists-and-ci-for-tests
jorgeMFS
authored
Improve Docker test script with local build fallback
jorgeMFS
committed
Merge pull request #17 from fix-docker-image-pull-error
jorgeMFS
authored
Fix Docker test input path
jorgeMFS
committed
Merge pull request #20 from jorgeMFS/8sa6ho-codex/fix-docker-image-build-error
jorgeMFS
authored
Add vcfx wrapper
jorgeMFS
committed
Add Docker entrypoint and path setup
jorgeMFS
committed
Merge pull request #22 from jorgeMFS/codex/fix-vcfx_validator-command-not-found-error
jorgeMFS
authored
Merge pull request #21 from jorgeMFS/codex/implement-vcfx-wrapper-with-argument-parsing
jorgeMFS
authored
fix docker tests to use bash
jorgeMFS
committed
Merge pull request #23 from jorgeMFS/codex/fix-test_docker-failure-in-build-process
jorgeMFS
authored

Commits on May 23, 2025

Fix validator passthrough
jorgeMFS
committed
Merge pull request #24 from fix-issue-in-docker-test-pipeline
jorgeMFS
authored
Simplify tool discovery in CMake
jorgeMFS
committed
Merge pull request #25 from refactor-add_subdirectory-and-vcfx_tools-logic
jorgeMFS
authored
Fix macOS test failures
jorgeMFS
committed
Merge pull request #28 from jorgeMFS/codex/update-build-test.yml-for-cross-platform-testing
jorgeMFS
authored
fix: avoid duplicate add_subdirectory on case-insensitive FS
jorgeMFS
committed
Merge pull request #29 from jorgeMFS/codex/fix-cmake-build-errors-with-vcfx_wrapper
jorgeMFS
authored
Fix Windows getopt
jorgeMFS
committed
Merge pull request #32 from fix-zlib-installation-failure-in-build
jorgeMFS
authored
fix: use cmake parallel build
jorgeMFS
committed
Merge branch 'main' into codex/fix-zlib-installation-failure-in-build
jorgeMFS
authored
Merge pull request #33 from jorgeMFS/codex/fix-zlib-installation-failure-in-build
jorgeMFS
authored
Fix Windows build by installing getopt
jorgeMFS
committed
Merge pull request #34 from jorgeMFS/codex/fix-missing-getopt.h-and-getopt.lib
jorgeMFS
authored
Remove Windows references
jorgeMFS
committed
Merge pull request #35 from jorgeMFS/codex/resolve-missing-getopt.lib-and-header-errors
jorgeMFS
authored
feat: add --version support across tools
jorgeMFS
committed
Merge pull request #36 from jorgeMFS/codex/find-features-to-improve-the-code
jorgeMFS
authored
fix alt mismatch logic
jorgeMFS
committed
Merge pull request #37 from update-alt-discrepancy-check-and-tests
jorgeMFS
authored
Ignore genotype query test artifacts
jorgeMFS
committed
Merge pull request #38 from jorgeMFS/8nw2ij-codex/update-test-paths-and-clean-up-directory
jorgeMFS
authored
Ignore temporary test outputs
jorgeMFS
committed
Merge pull request #39 from jorgeMFS/1957s6-codex/update-.gitignore-and-clean-tests/tmp
jorgeMFS
authored
Fix ALT normalization with colon in duplicate remover
jorgeMFS
committed
Support 64-bit positions in indexer
jorgeMFS
committed
Merge pull request #40
jorgeMFS
authored
Merge pull request #41 from change-position-variable-to-int64_t
jorgeMFS
authored
Refactor variant counter to stream input
jorgeMFS
committed
Merge pull request #42 from refactor-vcfx_variant_counter-and-read_maybe_compressed
jorgeMFS
authored
fix CSV quote escaping
jorgeMFS
committed
Merge pull request #43
jorgeMFS
authored
docs: update phred_filter usage
jorgeMFS
committed
Merge pull request #44 from jorgeMFS/codex/update-filter-options-in-docs
jorgeMFS
authored
fix test_variant_counter script path
jorgeMFS
committed
Merge pull request #47 from fix-bug-in-important-codebase-section
jorgeMFS
authored
Merge main
jorgeMFS
committed
Merge branch 'main' into codex/update-command-examples-in-docs
jorgeMFS
authored
Merge pull request #48 from update-command-examples-in-docs
jorgeMFS
authored
docs: document --version flag
jorgeMFS
committed
Merge pull request #49 from insert-version-flag-in-options-table
jorgeMFS
authored
Clarify version flag note
jorgeMFS
committed
Merge pull request #50 variant-flag-documentation-and-source
jorgeMFS
authored
docs: adjust toolkit utility count
jorgeMFS
committed
docs: add annotation and processing sections
jorgeMFS
committed
Merge pull request #52 from jorgeMFS/codex/update-docs/index.md-with-new-sections
jorgeMFS
authored
Merge pull request #51 from update-citation-wording-in-docs/citation.md
jorgeMFS
authored
docs: rename heading for sample comparison
jorgeMFS
committed
Merge pull request #53 from jorgeMFS/codex/update-vcf-comparison-commands-and-documentation
jorgeMFS
authored
Improve dark mode
jorgeMFS
committed
Merge pull request #54 from jorgeMFS/codex/improve-dark-mode-readability-and-colors
jorgeMFS
authored
Fix Python bindings
jorgeMFS
committed
Merge pull request #55 from implement-python-bindings-with-cmake-and-packaging
jorgeMFS
authored

Commits on May 24, 2025

Fix Docker build by installing Python dev deps
jorgeMFS
committed
Merge pull request #56 from fix-python3-installation-for-docker-build
jorgeMFS
authored
Add Python wrappers and wheel workflow
jorgeMFS
committed
Merge pull request #57 -Add Python wrappers and wheel CI
jorgeMFS
authored
Extend Python bindings
jorgeMFS
committed
Merge pull request #58 - extend-python-bindings
jorgeMFS
authored
Add vcfx wrapper test
jorgeMFS
committed
Merge pull request #59 from jorgeMFS/enhance-vcfx-with-help-and-list-commands
jorgeMFS
authored
Fix YAML syntax in workflow
jorgeMFS
committed
Merge pull request #60 fix-yaml-syntax-error-on-line-86
jorgeMFS
authored

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