This fork of delfi_scripts is for benchmarking against the DELFI method (short/long fragment ratios in 5mb bins). While we have attempted to stay as true to the original approach as possible, the following changes have been made:

1. We have made it runnable with the HG38 assembly.

2. We have removed the summary statistics, as we only want the feature creation. We run the cross-validation in python to have the same setup for all benchmarks.

3. We have ignored the z-scores (a meaasure of chromosome-arm-specific copy number changes). In the paper, these do not add significantly to the model AUC.

4. The features are saved as a csv file, so we can read them into python more easily. The feature creation is performed directly in 04-5mb_bins.r instead of 06-gbm_full.r.

5. Added/replaced command line arguments to use optparse and handle in- and output files in parent workflow.

6. GC correction failed when the GC content (bias argument) had NAs. So we set them to the median value.

7. Extraction of GC contents per fragment required insane amounts of RAM (>512gb available for some files), so we replaced the original approach with the one used in DELFI Lucas (later paper).

8. When summing across the 50 100kbp bins at a time, we ignore NAs instead of making the full 5mbp bin NA. This should reduce the number of 5mbp bins that are NA leading to removal of entire bins (which is problematic in a cross-dataset context when the test set has new NAs - would require imputation or similar).