PR Log

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.