Code

Dev#27

Code

Merged

rob-p merged 32 commits intomainCOMBINE-lab/oarfish:mainfrom devCOMBINE-lab/oarfish:devCopy head branch name to clipboardAug 26, 2024

+1,864-419

Commits

Commits on Aug 6, 2024

• starting to hack on some things

  

  Rob Patro

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  6809473

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Commits on Aug 7, 2024

• some more progress

  

  Rob Patro

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  4e94517

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• some single-cell impl ideas

  

  Rob Patro

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  e02f2df

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• cleanup

  

  Rob Patro

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  63f4f64

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• refactoring

  

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  5f1cc46

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• make clippy happy

  

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  f4a5a59

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• be quiet during single-cell em

  

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  990ebea

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Commits on Aug 8, 2024

• should be getting there

  

  Rob Patro

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  d764b92

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Commits on Aug 9, 2024

• more refactoring

  

  Rob Patro

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  c5a58a7

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• sort to put primary alignment first

  

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  0729dfb

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• docs

  

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  5d7326c

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• Docs

  

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  c648aab

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• change name of output file

  

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  c440f6d

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Commits on Aug 17, 2024

• New features

  Show description for 8d3ee95
  

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  8d3ee95

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• make sequencing tech Optional so it's only required with reads

  

  Rob Patro

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  3333625

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• more code docs

  

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  efa5340

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• simplify aligner code

  

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  aa1dee1

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• change seed to 11

  

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  21a514f

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Commits on Aug 18, 2024

• cleanup and refactor

  

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  cb1959f

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• track alignment source in output

  

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  c5374f4

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• fix obo

  

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  5b09b43

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Commits on Aug 19, 2024

• swith minimap2-rs upstream back to original source

  

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  committed
  bf28f9b

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Commits on Aug 25, 2024

• supp alignments match command-line minimap2

  

  Rob Patro

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  19d3918

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• add command line conflict for --reads with --single-cell

  

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  ddec48d

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• add pacbio-hifi, add best-n argument

  

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  86a5d80

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• improve help heading

  

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  cc99625

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Commits on Aug 26, 2024

• allow a list of more than one read files

  

  Rob Patro

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  da18481

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• add nice progress ticker

  

  Rob Patro

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  e3cbf46

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• fancy progress tickers

  

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  e156657

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• rely on upstream crate

  

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  0c70369

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• add finish message to progress bar in alignment mode

  

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  32312a0

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• bump versions

  

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  878571d

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