v0.2.1

[v0.2.1] - 2024-08-13

Added

• Added the --max_obs_trace argument to the parser. This can be used to manually set the maximum number of observations to trace. Useful for rerunning with a larger value on a subset of (previouslytruncated) reads. This overrides the value in the config file.
• When the min_obs_adapter value is detected as the adapter_end in the llr workflow, a second round of llr gains (starting from min_obs_adapter) is calculated to refine the adapter_end detection.
• Detect results contain information on full read length and preload size.
• Added a debug_logger object in the llr workflow.
• Added a refine_max_adapter_end_adjust parameter to the llr workflow configuration. When the suggested adjusted in the refinement is more than this value, the refinement is skipped. Default is 250.
• Added a --config flag to the parser. This can be used to specify the latest default config TOML file.

Fixed

• Signal preload: signal preload size is now explicitly updated based on the max_obs_trace value after initializing the config object.
• Partition stats: partition (adapter, polya, preloaded_rna) stats are now computed for the adapter based on the llr-detected boundary, and no longer becomes None when the mvs workflow fails in the combined detection.
• setup.py: fixed the package import to correctly find all packages and sub-packages.
• setup.py: added a config_files folder to the package data.

Changed

• Renamed rna partition stats (start, len, mean, std, med, mad) to preloaded_rna to clarify that they are computed from the preloaded RNA signal, not the full read signal.
• adapter_end defaults to the value detected in the llr workflow, also when the mvs workflow fails in the combined detection (previously defaulted to None).
• preloaded_rna partition stats are None in the case of truncated polya signals.
• Median shift calculation in mvs workflow is now done using the median of the detected adapter signal as a whole, instead of the median of a specified window.
• The ADAPTed version is now part of the created output dirctory name.
• The parser now requires a valid configuration file (--config) or a chemistry (--chemistry) to be provided.
• Parameters for RNA002:
  • min_obs_adapter = 2000 (previously 2500)
  • max_obs_trace = 12000 (previously 8000)
  • adapter_trace_stride = 50 (previously 40)
  • adapter_trace_early_stop_stride = 500 (previously 1000)
  • polya_trace_early_stop_stride = 50 (previously 40)
  • polyA_local_range = [0.0, 12.0] (previously [0.0, 10.0])