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onr1.2

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Commits on Feb 28, 2023

• Fix deepconsensus filter_reads cli.

  

  anastasiyabl

  authored and

  Copybara-Service

  committedFeb 28, 2023
  82df652

Commits on Feb 27, 2023

• Add filter_reads capability to DeepConsensus CLI.

  

  kishwarshafin

  authored and

  Copybara-Service

  committedFeb 27, 2023
  06f08a7

Commits on Feb 24, 2023

• Get ccs_seqname from the a aligned reference rather than constructing it from the subread.

  

  danielecook

  authored and

  Copybara-Service

  committedFeb 24, 2023
  d3c94f0

Commits on Feb 17, 2023

• Update version numbers for v1.2.

  

  anastasiyabl

  authored and

  Copybara-Service

  committedFeb 17, 2023
  77798d6

Commits on Feb 10, 2023

• Enable making tf examples with maize data.

  

  anastasiyabl

  authored and

  Copybara-Service

  committedFeb 10, 2023
  c11b5a1

• Update python formatting.

  

  danielecook

  authored and

  Copybara-Service

  committedFeb 10, 2023
  b5546cd

Commits on Feb 8, 2023

• Uncap base quality scores to 93 by default.

  

  anastasiyabl

  authored and

  Copybara-Service

  committedFeb 8, 2023
  8b87555

Commits on Feb 2, 2023

• Fix location of ccs bq embedding layer.

  

  danielecook

  authored and

  Copybara-Service

  committedFeb 2, 2023
  02274ba

Commits on Jan 31, 2023

• Finalize CCS BQ Integration.

  

  danielecook

  authored and

  Copybara-Service

  committedJan 31, 2023
  63df275

• Silence some pytype errors.

  

  Genomics team in Google Health

  authored and

  Copybara-Service

  committedJan 31, 2023
  b403905

Commits on Jan 30, 2023

• Add flag for generating tf examples with ccs base quality scores.

  

  danielecook

  authored and

  Copybara-Service

  committedJan 30, 2023
  c0b43d5

Commits on Jan 27, 2023

• Add profiling scope.

  

  danielecook

  authored and

  Copybara-Service

  committedJan 27, 2023
  d482ca0

• Modify get_indices to handle ccs_bq scores.

  

  danielecook

  authored and

  Copybara-Service

  committedJan 27, 2023
  5c09997

Commits on Jan 26, 2023

• Modify total_rows calculation to account for base quality scores.

  

  danielecook

  authored and

  Copybara-Service

  committedJan 26, 2023
  3884c05

Commits on Jan 25, 2023

• Allow for base quality scores to be processed by example generation pipeline.

  

  danielecook

  authored and

  Copybara-Service

  committedJan 25, 2023
  da89777

Commits on Jan 12, 2023

• Internal Updates

  

  danielecook

  authored and

  Copybara-Service

  committedJan 12, 2023
  55ef05e

Commits on Jan 4, 2023

• Move params.vocab_size to dc_constants.VOCAB_SIZE.

  

  danielecook

  authored and

  Copybara-Service

  committedJan 4, 2023
  d9d709c

Commits on Jan 3, 2023

• Internal Update

  

  danielecook

  authored and

  Copybara-Service

  committedJan 3, 2023
  2b8f061

Commits on Dec 20, 2022

• Use ReZero instead of LayerNorms.

  

  Genomics team in Google Health

  authored and

  Copybara-Service

  committedDec 20, 2022
  01a4e1c

• Fix inconsistent training steps.

  

  Genomics team in Google Health

  authored and

  Copybara-Service

  committedDec 20, 2022
  09d3660

• Remove todo.

  

  danielecook

  authored and

  Copybara-Service

  committedDec 20, 2022
  0023941

Commits on Dec 15, 2022

• [NumPy] Remove references to deprecated NumPy type aliases.

  

  Genomics team in Google Health

  authored and

  Copybara-Service

  committedDec 15, 2022
  c28cd1f

Commits on Dec 14, 2022

• Fix warnings.

  

  anastasiyabl

  authored and

  Copybara-Service

  committedDec 14, 2022
  6b6243c

Commits on Dec 13, 2022

• Update version numbers for v1.1.

  

  anastasiyabl

  authored and

  Copybara-Service

  committedDec 13, 2022
  63d7e03

Commits on Dec 8, 2022

• Update the config with values used in v1.1.

  

  anastasiyabl

  authored and

  Copybara-Service

  committedDec 8, 2022
  35d295b

Commits on Nov 21, 2022

• Pin everything. This is to address the pip install issue in #48 mentioned by @mjg0.

  

  pichuan

  authored and

  Copybara-Service

  committedNov 21, 2022
  be308d0

Commits on Nov 14, 2022

• Optional partition by PacBio smart windows

  

  akolesnikov

  authored and

  Copybara-Service

  committedNov 14, 2022
  d1fc534

Commits on Nov 2, 2022

• Restore from latest checkpoint instead of the checkpoint at epoch beginning.

  

  anastasiyabl

  authored and

  Copybara-Service

  committedNov 2, 2022
  71f88dd

Commits on Oct 23, 2022

• Mask-based local sliding window attention.

  

  Genomics team in Google Health

  authored and

  Copybara-Service

  committedOct 23, 2022
  b8dfd6a

Commits on Oct 13, 2022

• Update params to match the chosen model for DC 1.0 release.

  

  anastasiyabl

  authored and

  Copybara-Service

  committedOct 13, 2022
  16d2762

Commits on Oct 11, 2022

• Output counters in inference mode.

  

  akolesnikov

  authored and

  Copybara-Service

  committedOct 11, 2022
  4662140

Commits on Oct 4, 2022

• Restructure calibrate lib for better re-use. Add --dc_calibrate flag.

  

  danielecook

  authored and

  Copybara-Service

  committedOct 4, 2022
  c3eda54

• Fix attention layer init.

  

  Genomics team in Google Health

  authored and

  Copybara-Service

  committedOct 4, 2022
  a66e3a1

Commits on Sep 26, 2022

• Small fix to remove @ prefix from bam read names.

  

  danielecook

  authored and

  Copybara-Service

  committedSep 26, 2022
  c04a86a

Commits on Sep 24, 2022

• Add RG tags to BAM output

  

  danielecook

  authored and

  Copybara-Service

  committedSep 24, 2022
  5f75175

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