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.*
• #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
• #16: Add a script for making the distance index with -w to try and force the top-level chain to include nodes with all sample haplotypes *This could be more flexible in choosing the nodes because if a path is fragmented it won't find any nodes, but it depends a lot on the graph and it works for now
• #17: Add more robust parsing condition for VCF file and unify input graph arg
• #18: Make sure that all paths get indexed for the path position overlay
• #19: Fix bug where BH correction overwrites a column
• #21: Write snarl path partitions to a file and multithread stoat graph