SUMMARY snakesee cli constants estimation data_loader estimator pending_inferrer rule_matcher estimator events exceptions formatting log_handler_script logging models parameter_validation parser core failure_tracker file_position job_tracker line_parser log_reader metadata patterns stats utils persistence backend db fs plugins base bwa discovery fastp fgbio loader registry samtools star profile state clock config job_registry paths rule_registry workflow_state state_comparison tui accessibility monitor types utils validation variance