dysgu_dev <- master #108
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dysgu_dev <- master #108
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Merge pull request #97 from kcleal/master
It seems like at some point the usage of update_filter_value changed, because in several spots, it is missing the sample_name argument. This breaks `dysgu filter --keep-all`.
correct usage of update_filter_value in filter_normals
* v1.6.6 updated README * Update main.yml * Added pyproject.toml * Updated pyproject.toml and setup.py
kcleal
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Oct 24, 2024
* dysgu_dev <- master (#108) * correct usage of update_filter_value in filter_normals It seems like at some point the usage of update_filter_value changed, because in several spots, it is missing the sample_name argument. This breaks `dysgu filter --keep-all`. * Update main.yml * Update main.yml * Update requirements.txt * updated build process to pyproject.toml (#103) * v1.6.6 updated README * Update main.yml * Added pyproject.toml * Updated pyproject.toml and setup.py * Update pyproject.toml --------- Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com> * Better recall+precision for long-reads. Improved merging pipeline. Faster runtime. Code refactoring. WIP # [skip ci] * Fixed issues with overriding presets. --mode option updated # [skip ci] * Fixed issues with overriding presets. --mode option updated to support r10 and revio, new presets available. --no-gt flat removed # [skip ci] * Fixed CLI issues for tests # [skip ci] * Fixed API issue --------- Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com>
kcleal
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Oct 24, 2024
* dysgu_dev <- master (#108) * correct usage of update_filter_value in filter_normals It seems like at some point the usage of update_filter_value changed, because in several spots, it is missing the sample_name argument. This breaks `dysgu filter --keep-all`. * Update main.yml * Update main.yml * Update requirements.txt * updated build process to pyproject.toml (#103) * v1.6.6 updated README * Update main.yml * Added pyproject.toml * Updated pyproject.toml and setup.py * Update pyproject.toml --------- Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com> * Better recall+precision for long-reads. Improved merging pipeline. Faster runtime. Code refactoring. WIP # [skip ci] * Fixed issues with overriding presets. --mode option updated # [skip ci] * Fixed issues with overriding presets. --mode option updated to support r10 and revio, new presets available. --no-gt flat removed # [skip ci] * Fixed CLI issues for tests # [skip ci] * Fixed API issue * v1.7.0 * added deprecated warning for mode --------- Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com>
kcleal
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Oct 25, 2024
* dysgu_dev <- master (#108) * correct usage of update_filter_value in filter_normals It seems like at some point the usage of update_filter_value changed, because in several spots, it is missing the sample_name argument. This breaks `dysgu filter --keep-all`. * Update main.yml * Update main.yml * Update requirements.txt * updated build process to pyproject.toml (#103) * v1.6.6 updated README * Update main.yml * Added pyproject.toml * Updated pyproject.toml and setup.py * Update pyproject.toml --------- Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com> * Better recall+precision for long-reads. Improved merging pipeline. Faster runtime. Code refactoring. WIP # [skip ci] * Fixed issues with overriding presets. --mode option updated # [skip ci] * Fixed issues with overriding presets. --mode option updated to support r10 and revio, new presets available. --no-gt flat removed # [skip ci] * Fixed CLI issues for tests # [skip ci] * Fixed API issue * v1.7.0 * added deprecated warning for mode * Added filter for high divergence reads (long-reads only) # [skip ci] --------- Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com>
kcleal
added a commit
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Nov 20, 2024
* dysgu_dev <- master (#108) * correct usage of update_filter_value in filter_normals It seems like at some point the usage of update_filter_value changed, because in several spots, it is missing the sample_name argument. This breaks `dysgu filter --keep-all`. * Update main.yml * Update main.yml * Update requirements.txt * updated build process to pyproject.toml (#103) * v1.6.6 updated README * Update main.yml * Added pyproject.toml * Updated pyproject.toml and setup.py * Update pyproject.toml --------- Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com> * Better recall+precision for long-reads. Improved merging pipeline. Faster runtime. Code refactoring. WIP # [skip ci] * Fixed issues with overriding presets. --mode option updated # [skip ci] * Fixed issues with overriding presets. --mode option updated to support r10 and revio, new presets available. --no-gt flat removed # [skip ci] * Fixed CLI issues for tests # [skip ci] * Fixed API issue * v1.7.0 * added deprecated warning for mode * Added filter for high divergence reads (long-reads only) # [skip ci] * Better read merging for long reads. New clustering methods for long reads. Improved runtime. * Update main.yml * Update main.yml * Update osx-deps * Update main.yml macos11 * Update main.yml * Update main.yml * Update main.yml * Update osx-deps * Update osx-deps * Update osx-deps * Update osx-deps * Update main.yml * Update osx-deps * Update main.yml * Updated workflow * Updated workflow * Updated workflow * Update main.yml * Updated workflow --------- Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com>
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