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Commits on Sep 9, 2021

• Remove trailing slash.

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  danielecook

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Commits on Sep 4, 2021

• Internal change

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  kishwarshafin

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Commits on Aug 26, 2021

• Updating the flag description to reflect that --use_fast_pass_aligner should always be True. Refactor the checking code to be more readable.

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  pichuan

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Commits on Aug 24, 2021

• Run automated linter on C++ code.

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  MariaNattestad

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Commits on Aug 23, 2021

• Resolve String Error Code Usages

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  Genomics team in Google Health

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Commits on Aug 19, 2021

• Resolve String Error Code Usages

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  Genomics team in Google Health

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Commits on Aug 11, 2021

• Upgrade Nucleus to support TF 2.6.0.

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  cmclean

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• Fix a string constant that was breaking the build.

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  pichuan

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Commits on Aug 10, 2021

• internal updates

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  danielecook

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• Update Nucleus to allow (optionally) keeping only the specified auxiliary tags.

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  pichuan

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Commits on Aug 9, 2021

• Relax the constraint for input truth VCF to skip 0/0 entries, instead of raising an error.

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  danielecook

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Commits on Aug 6, 2021

• Add an variable in build_clif.sh so that we can optionally pin CLIF version as needed.

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  pichuan

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• Update our DeepTrio case study GLnexus config to be DeepVariant_unfiltered.

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  pichuan

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• Temporarily disable usage of tensorflow error code string representation

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  Genomics team in Google Health

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• Get Nucleus to build on Ubuntu20.04, with Python3.8.

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  pichuan

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Commits on Aug 5, 2021

• Remove RandomGuess model

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  danielecook

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• Don't depend on Tensorflow's error code string representation in tests,

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  Genomics team in Google Health

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Commits on Jul 31, 2021

• Header for direct phasing class.

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  akolesnikov

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Commits on Jul 29, 2021

• Update version.

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  pichuan

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• Update to a valid link.

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  pichuan

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• Update version.

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  pichuan

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• Update metrics-deeptrio.md.

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  pichuan

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Commits on Jul 27, 2021

• Update deeptrio training data.

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  pichuan

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• Update the version links in the Python notebooks to be r1.2.

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  pichuan

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• Add documentation for --include_med_dp.

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  pichuan

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• Update metrics.md.

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  pichuan

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Commits on Jul 26, 2021

• Fix breakage affecting DeepTrio in duo mode and add unit tests for duos.

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  MariaNattestad

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• Adapt runtime_by_region stats for multi-sample, so it works for DeepTrio.

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  MariaNattestad

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• Update documents with latest version (1.2.0).

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  pichuan

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• Update more *-case-study.md.

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  pichuan

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Commits on Jul 25, 2021

• Update a few *-case-study.md files.

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  pichuan

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• Update Quick Starts.

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  pichuan

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Commits on Jul 24, 2021

• Update version in comments.

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  pichuan

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Commits on Jul 23, 2021

• Fix paths in DeepTrio Dockerfile, removing "-rc1" for pacbio models.

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  MariaNattestad

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• Enable --runtime_report in run_deeptrio and add to inference scripts for versions that support it.

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  MariaNattestad

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