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Xian Chang edited this page Sep 12, 2025 · 16 revisions

This tracks all PRs made since the last Stoat Report. Ideally we should add a summary of each PR to be added to the report and clear the log once the report is done.

Changes since last report (27/08/25)

  • #7: Simulation lr
  • #8: Change the stoat graph subcommand to take the same binary phenotype file as stoat vcf
  • #9: Switch old uncompiled debug code to new logger
  • #10: Refactor the partitioning code to use the same code path for regular snarls and irregular snarls.
    • Also add a way to use assert() with the logger
  • #11: Handle special case collinearity lr, Remove BH & top variant file from natif stoat vcf/graph, add verbosity BH, remove LOG_FATAL replaced by throw, Add namespace stoat in stat_test.*
  • #12: Change the actual stoat lr implementation by the mathematical one, correct filtration, handle new specific table regression case (pseudo inversion needed).
  • #15: Fix bug in stoat graph looking at paths we didn't include

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