Release v0.2.3 · KleistLab/ADAPTed

[v0.2.3] - 2024-11-13

Mysterious runtime warnings occuring in the mvs polya workflow were identified as being due to too short signals. These signals are now filtered out before the detection workflow.
Run time warnings during peak detection are now filtered.

A new detection workflow is added that uses a CNN to predict the boundaries of the adapter and polyA signals. The CNN method replaces the previous llr workflow as the primary detection method and provides faster detection. The CNN workflow comes with a depency on torch (combined_detect_cnn).
SigProcConfig now has a primary_config attribute that is set at runtime to describe the detection workflow used prior to validation.
Introduction of a new combined_detect_llr2 function that uses a downscaled signal for the llr workflow, with a split peak correction for the polyA trace.
The combined_detect_cnn function now has a fallback to a quick version of the llr method if validation of the boundary predictions fails.

config.batch.bidx_passed/failed is now config.batch.batch_idx_pass/fail.
default minibatch size is now 1000.
combined_detect has been renamed to combined_detect_llr.
ReadResult, DetectResults and Boundaries have been moved to adapted.container_types.
Preloaded signals that are shorter than the preload size are now padded with nans instead of zeros.
Mad winsorization by imputing outliers with local medians has been changed to mad winsorization by clipping.
The flag for setting the num_proc in the parser has been changed to -j.
Introduction of the 'core' SigProcConfig section that contains parameters that are used across multiple detection methods in the code.
sig_norm_outlier_thresh has been moved to the new core section, as have adapter, trace and polya min/max obs parameters.
The llr_helpers module has been merged into the llr module.

The Task attribute of the Config object is removed.
The save_llr_trace parser argument is removed.
Functions for mad winsorization by imputing outliers with local medians (impute_window_median, mad_outlier_indices, mad_normalize, mad_winsor) are removed.
The sig_norm_winsor_window LLRBoundariesConfig attribute is removed.