Code

feat: add translation of alignment#78

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gordonkoehn wants to merge 29 commits intomaincbg-ethz/sr2silo:mainfrom feat/translate_aligncbg-ethz/sr2silo:feat/translate_alignCopy head branch name to clipboard

+16,430-33

Commits

Commits on Jan 10, 2025

• module scope correction

  

  Gordon J. Köhn

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  31edc97

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Commits on Jan 16, 2025

• implement process/normalize_reads()

  

  Gordon J. Köhn

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  5fc82ec

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• WIP: bam_to_cleartext_alignment

  

  Gordon J. Köhn

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  58e753c

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• POC bam_to_cleartext_aligment()

  

  Gordon J. Köhn

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• WIP insertions as JSON

  

  Gordon J. Köhn

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  dd22531

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• POC full aligne wiht padding and small data

  

  Gordon J. Köhn

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  95b1d79

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• add note

  

  Gordon J. Köhn

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  43a9870

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• correct readme and cleanup of index files

  

  Gordon J. Köhn

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• reformat

  

  Gordon J. Köhn

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  7a35336

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• refactor resources

  

  Gordon J. Köhn

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Commits on Jan 23, 2025

• Merge branch 'main' into feat/translate_align

  gordonkoehn

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  7fdbbcb

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• enhance docstring

  

  Gordon J. Köhn

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  e24af7e

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• make nextclade input

  

  Gordon J. Köhn

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  60b91c5

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• adding nextclade binding as submodule

  

  Gordon J. Köhn

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• run from pyhton

  

  Gordon J. Köhn

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• getting sequences types

  

  Gordon J. Köhn

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• succesfuly load genemap

  

  Gordon J. Köhn

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  53e21af

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• got ref_translation

  

  Gordon J. Köhn

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  b7ea5ba

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• got coordsMap

  

  Gordon J. Köhn

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  4501589

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• got aligment range

  

  Gordon J. Köhn

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• get all params for translate_genes

  

  Gordon J. Köhn

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• translation works

  

  Gordon J. Köhn

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Commits on Jan 28, 2025

• got AA changes

  

  Gordon J. Köhn

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  217e7d5

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• output AA changes

  

  Gordon J. Köhn

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• test process more

  

  Gordon J. Köhn

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  d9dc8ec

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• factored out the translation for one seqeunce in nextclade

  

  Gordon J. Köhn

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  684f8b7

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• for many seqs

  

  Gordon J. Köhn

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• batch failing

  

  Gordon J. Köhn

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  d2293b9

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• added read_id and orignal sequence to rust // python side needs updating

  

  Gordon J. Köhn

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  fea715c

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