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Commits on Jun 2, 2022

• Update 2 remaining docs for v1.4.0 release.

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• Update remaining docs for v1.4.0 release.

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Commits on Jun 1, 2022

• Update to v1.4.0 in DeepTrio documentations.

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• Update to v1.4.0 in DeepVariant documentations.

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• Update version in deeptrio testdata. This doesn't affect the code.

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• Update DeepVariant metrics.md after Dockerfile points to the final model locations.

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Commits on May 31, 2022

• Finalize the v1.4.0 models for DeepVariant and DeepTrio. Update all references of 1.3.0 or r1.3 to the latest version.

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Commits on May 27, 2022

• Add a mention of the user question in google#505.

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• Clean up Dockerfile.

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• Set the default value of phase_reads_region_padding and phase_max_reads. Make sure these two flags are only used when phase_reads is true.

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• Update the DV PacBio case study file to be the unphased BAM.

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Commits on May 26, 2022

• Refactor code for generating and writing out examples into a function.

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• Add a --example_info_json option for freeze_graph.py

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• Added an alternative shuffling option.

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Commits on May 25, 2022

• Update show_examples to use the *example_info.json information.

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Commits on May 24, 2022

• Udpate DeepVariant PB: --max_reads_per_partition=600 and --phase_max_candidates=5000, and update metrics.md accordingly.

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Commits on May 23, 2022

• Fix a bug where the BAM_{CHILD,PARENT1,PARENT2} are not correctly passed in.

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• Add parent and child specific customized_model flags for DeepTrio.

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• Fix the way the model ckpt example_info.json file is copied. Currently the assumption is that the information lives in a file model.ckpt.example_info.json under the same directory that the model …

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• Fix a bug related to direct phasing - when padding is not set, we should query just from region, not padded_region.

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Commits on May 19, 2022

• Clean up a logging information (v2) with a variable that no longer exists after refactoring.

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• Refactor the examples generation code to avoid having to store all examples in memory.

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• Small refactoring - move local variables closer to the code block where they are used.

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Commits on May 18, 2022

• Add phase_max_candidates: If the number of candidates exceeds this number in a window, skip direct phasing.

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• Fix an issue where the sample is not in scope, but ends up referencing the last one in the last for loop.

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Commits on May 15, 2022

• Improve run-prereq.sh and BUILD file, fixing a runtime issue.

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Commits on May 12, 2022

• Copy example_info.json (if exists) to the output directory of the shuffle script, and update the training tutorial.

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Commits on May 10, 2022

• Starting in DeepTrio in release v1.4:

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Commits on May 9, 2022

• Update call_variants.py to use model.ckpt.input_info file. Currently it's still not requiring the file to exist. We can make this strict later as needed.

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• Remove image/format because we end up never using a separate format.

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• Update all DeepVariant models to the latest release candidates.

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Commits on May 6, 2022

• Only copy the *example_info.json file if the target doesn't already

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Commits on May 5, 2022

• Automated g4 rollback of changelist 404595398

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• Update DeepVariant Dockerfile to use the latest PacBio and Hybrid release candidates. Update metrics.md accordingly.

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Commits on May 4, 2022

• Update our default 64 core machines to simply use n1-standard-64 (64 cores, 240GB RAM).

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