Code

PED file validation#587

Code

Merged

epiercehoffman merged 14 commits intomainbroadinstitute/gatk-sv:mainfrom eph_validate_pedbroadinstitute/gatk-sv:eph_validate_pedCopy head branch name to clipboardAug 29, 2023

+215-6

Commits

Commits on Aug 17, 2023

• add ValidatePedFile task & script

  epiercehoffman

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  60c09a1

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• update ped file docs

  epiercehoffman

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  021f2ee

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• add summary to top of ped validation script

  epiercehoffman

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  8e0db42

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• formatting

  epiercehoffman

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  0c923e7

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• write to stderr for success too

  epiercehoffman

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  7bef5b4

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• linting

  epiercehoffman

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  6dab052

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• output ped from ValidatePedFile to enforce order of execution

  epiercehoffman

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Commits on Aug 18, 2023

• write success message to stdout instead of stderr

  epiercehoffman

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  8decb1f

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• write success message to stdout instead of stderr

  epiercehoffman

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  ea8aeb5

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• add internal links to website for ped format & sample id requirements

  epiercehoffman

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Commits on Aug 21, 2023

• check for empty samples list, no spaces in column names, add note on headers

  epiercehoffman

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Commits on Aug 23, 2023

• require 0, 1, or 2 for sex (not just integer)

  epiercehoffman

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  28a68f4

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• define constants for id_type, move parent ID==0 check to validate_id

  epiercehoffman

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  db7cc5a

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Commits on Aug 29, 2023

• require exactly 6 columns. fix invocation of script in task

  epiercehoffman

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  5b3280f

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