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speed up merge script when deep pedigrees are present#6168

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lukasmueller wants to merge 10 commits into
masterfrom
topic/speed_up_merge_script
Open

speed up merge script when deep pedigrees are present#6168
lukasmueller wants to merge 10 commits into
masterfrom
topic/speed_up_merge_script

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@lukasmueller

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when pedigrees are large, the merge function will try to parse the entire pedigree for both parents, which is very slow. It only needs the direct parents. Copied a function from CXGN::Chado::Stock called get_direct_parents and modified it slightly for easier data processing later. Changed merge function to use the new function.

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Checklist

  • Refactoring only
  • Documentation only
  • Fixture update only
  • Bug fix
    • The relevant issue has been closed.
    • Further work is required.
  • New feature
    • Relevant tests have been created and run.
    • Data was added to the fixture
      • Data was added via a patch in /t/data/fixture/patches/.
    • User-Facing Change
      • The user manual in /docs has been updated.
    • Any new Perl has been documented using perldoc.
    • Any new JavaScript has been documented using JSDoc.
    • Any new legacy JavaScript has been moved from /js to /js/source/legacy.

…tire pedigree for both parents, which is very slow. It only needs the direct parents. Copied a function from CXGN::Chado::Stock called get_direct_parents and modified it slightly for easier data processing later. Changed merge function to use the new function.
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5 participants