Commits

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 r1.2

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danielecook

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Commit History

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 10, 2023

• Update python formatting.

  

  danielecook

  authored and

  Copybara-Service

  committedFeb 10, 2023
  b5546cd

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

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

• Remove todo.

  

  danielecook

  authored and

  Copybara-Service

  committedDec 20, 2022
  0023941

Commits on Oct 6, 2022

• Modify requirements

  

  danielecook

  authored and

  Copybara-Service

  committedOct 6, 2022
  e0e6d28

• Update inspecting examples colab.

  

  danielecook

  authored and

  Copybara-Service

  committedOct 6, 2022
  fb9dd7e

Commits on Oct 5, 2022

• Update assembly metrics for v1.0

  

  danielecook

  authored and

  Copybara-Service

  committedOct 5, 2022
  07160e8

Commits on Oct 4, 2022

• Update Quickstart.

  

  danielecook

  authored and

  Copybara-Service

  committedOct 4, 2022
  5eb0941

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

  

  danielecook

  authored and

  Copybara-Service

  committedOct 4, 2022
  c3eda54

Commits on Sep 30, 2022

• Update Yield metrics page for v1.0.

  

  danielecook

  authored and

  Copybara-Service

  committedSep 30, 2022
  73ec318

• Update Runtime metrics page.

  

  danielecook

  authored and

  Copybara-Service

  committedSep 30, 2022
  dacaef8

• Update to Python 3.9

  

  danielecook

  authored and

  Copybara-Service

  committedSep 30, 2022
  854b5bf

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

Commits on Sep 20, 2022

• Automate base quality calibration setting from model params.json

  

  danielecook

  authored and

  Copybara-Service

  committedSep 20, 2022
  2e178bc

• Configure Quick inference to output bam files.

  

  danielecook

  authored and

  Copybara-Service

  committedSep 20, 2022
  d9ada87

• Integrate aux tags into quick inference.

  

  danielecook

  authored and

  Copybara-Service

  committedSep 20, 2022
  e045008

Commits on Sep 16, 2022

• Bump version to v1.0.0

  

  danielecook

  authored and

  Copybara-Service

  committedSep 16, 2022
  2d42456

• Remove unnecessary setting of sn tag and avoid renaming object.

  

  danielecook

  authored and

  Copybara-Service

  committedSep 16, 2022
  10f46b6

Commits on Sep 13, 2022

• Remove padding operations from DeepConsensus.

  

  danielecook

  authored and

  Copybara-Service

  committedSep 13, 2022
  121a94c

Commits on Sep 12, 2022

• Carry over ec, np, rq tags (part 1).

  

  danielecook

  authored and

  Copybara-Service

  committedSep 12, 2022
  08a4292

• Count trimmed insertions

  

  danielecook

  authored and

  Copybara-Service

  committedSep 12, 2022
  3a8bd9a

• Remove unecessary np.array conversion.

  

  danielecook

  authored and

  Copybara-Service

  committedSep 12, 2022
  c0f8cc4

Commits on Sep 9, 2022

• Training improvements.

  

  danielecook

  authored and

  Copybara-Service

  committedSep 9, 2022
  8b9268c

• Skip performing padding on non-terminal windows.

  

  danielecook

  authored and

  Copybara-Service

  committedSep 9, 2022
  dcd2080

• Keep track of ins_trim value.

  

  danielecook

  authored and

  Copybara-Service

  committedSep 9, 2022
  41a990d

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